Zuzana Sajdlová
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Zuzana Sajdlová has a total of 64 co-authors. Here are the top co-authors by number of shared publications:
- Tomáš Jůza
Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
13 shared publications - Martin Čech
Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czech Republic
11 shared publications - Vladislav Draštík
Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czech Republic
10 shared publications - Petr Blabolil
Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czech Republic
9 shared publications - Jan Kubečka
Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 370 05 České Budějovice, Czech Republic
6 shared publications - Jiří Peterka
Institute of Hydrobiology Biology Centre of the Czech Academy of Sciences České Budějovice Czech Republic
6 shared publications
Latest Publications
- Open Access
- 22 June 2026
- Published by MDPI AG in Proceedings
- Vol. 146 (1) , 111
Longlines for Sampling, Reduction and Eradication of Large Alien Invasive Predatory Species: The Case of European Catfish
Introduction: Longlines are traditional fishing gear and are widely used in marine systems for both quantitative and qualitative sampling of large predators like tuna, swordfish, sailfish, marlin or sharks. This highly selective method has been applied for the sampling of European catfish (Silurus glanis), the largest freshwater fish in Europe. This apex predator is a highly valuable fish species in its native localities of Central and Eastern Europe (commercial fishing, anglers’ trophy fishing, biomanipulation purposes) but a dangerous alien invasive species in South and Western Europe. Objective: The efficiency and selectivity of longlines for European catfish sampling were compared with more traditional fishing methods like gillnets and electrofishing. Methodology: European catfish were sampled in native areas (Římov, Žlutice, Vrchlice, Hubenov, Lipno, Želivka reservoirs; Czech Republic) and areas of invasion (Lakes Campagna, Avigliana Grande, Maggiore; Italy; Belver, Meimoa, Cedillo reservoirs; Portugal; Iznajar, Mequinenza reservoirs; Spain) following the protocols of best catfish (Silurus glanis) capture methodologies in small and large lakes and reservoirs established for the current needs of the European Commission within the LIFE PREDATOR project. Results: The longline efficiency expressed as the proportion of individual hooks catching catfish (live baits exposed overnight) was from low to medium (5–25%; Czech reservoirs, Italian lakes, Meimoa reservoir) to very high (up to over 50%; Portuguese and Spanish reservoirs). In many water bodies, specifically in areas of invasion, catfish represented 100% of the longline catch (Campagna, Maggiore, Cedillo, Iznajar, Mequinenza). In the rest of the water bodies, the by-catch ranged from 2 to 20% with the highest values occurring in its native localities (due to the presence of large individuals of Northern pike, Esox lucius, another predatory fish in these systems). In areas of invasion, the inconsiderable by-catch was composed of other non-native predatory fish species like pikeperch (Sander lucioperca), European perch (Perca fluviatilis) or channel catfish (Ictalurus punctatus). Both the efficiency and selectivity of longlines were higher compared to gillnets and electrofishing, and longlines also caught larger catfish individuals. Conclusions: Longlines represent an efficient and extremely selective method for European catfish sampling, reduction and even eradication, especially in areas of invasion. Their usage, however, requires specific equipment, skills and also baits.
- 22 June 2026
- Published by MDPI AG in Proceedings
- Vol. 146 (1) , 111
Open AccessLonglines for Sampling, Reduction and Eradication of Large Alien Invasive Predatory Species: The Case of European Catfish
Introduction: Longlines are traditional fishing gear and are widely used in marine systems for both quantitative and qualitative sampling of large predators like tuna, swordfish, sailfish, marlin or sharks. This highly selective method has been applied for the sampling of European catfish (Silurus glanis), the largest freshwater fish in Europe. This apex predator is a highly valuable fish species in its native localities of Central and Eastern Europe (commercial fishing, anglers’ trophy fishing, biomanipulation purposes) but a dangerous alien invasive species in South and Western Europe. Objective: The efficiency and selectivity of longlines for European catfish sampling were compared with more traditional fishing methods like gillnets and electrofishing. Methodology: European catfish were sampled in native areas (Římov, Žlutice, Vrchlice, Hubenov, Lipno, Želivka reservoirs; Czech Republic) and areas of invasion (Lakes Campagna, Avigliana Grande, Maggiore; Italy; Belver, Meimoa, Cedillo reservoirs; Portugal; Iznajar, Mequinenza reservoirs; Spain) following the protocols of best catfish (Silurus glanis) capture methodologies in small and large lakes and reservoirs established for the current needs of the European Commission within the LIFE PREDATOR project. Results: The longline efficiency expressed as the proportion of individual hooks catching catfish (live baits exposed overnight) was from low to medium (5–25%; Czech reservoirs, Italian lakes, Meimoa reservoir) to very high (up to over 50%; Portuguese and Spanish reservoirs). In many water bodies, specifically in areas of invasion, catfish represented 100% of the longline catch (Campagna, Maggiore, Cedillo, Iznajar, Mequinenza). In the rest of the water bodies, the by-catch ranged from 2 to 20% with the highest values occurring in its native localities (due to the presence of large individuals of Northern pike, Esox lucius, another predatory fish in these systems). In areas of invasion, the inconsiderable by-catch was composed of other non-native predatory fish species like pikeperch (Sander lucioperca), European perch (Perca fluviatilis) or channel catfish (Ictalurus punctatus). Both the efficiency and selectivity of longlines were higher compared to gillnets and electrofishing, and longlines also caught larger catfish individuals. Conclusions: Longlines represent an efficient and extremely selective method for European catfish sampling, reduction and even eradication, especially in areas of invasion. Their usage, however, requires specific equipment, skills and also baits.
- Open Access
Hatched Late to Be Fed? Identifying the Origin of Late-Summer Pikeperch Cohorts Using Daily Otolith Increments
Effective fisheries management depends on a clear understanding of the recruitment dynamics of young-of-year (YOY) fish. Analysis of two-decade ichthyological data from Czechia and the Netherlands revealed an unexpectedly small cohort of YOY pikeperch (Sander lucioperca) in late summer. The origin of these individuals remained speculative. Building on the long-term patterns documented in these regions, we provide a new empirical contribution by analyzing the daily otolith increments of 29 pikeperch individuals sampled in the Lipno Reservoir (Czechia) in late August 2023. The otolith-based aging revealed that the extremely small pikeperch were not more than 35 days old, indicating they hatched at the turn of July and August. Even with the uncertainty in the exact timing of the first otolith increment formation, this approach disclosed the origin of the extremely small cohort as late-hatched individuals produced by wild late-spawning pikeperch. These extremely small, delayed pikeperch coexist with their normal, earlier-spawned conspecifics, which are often already piscivorous. Although they mostly do not survive the first winter, they still contribute to the recruitment indirectly by serving as prey for conspecifics. Our results highlight the need to revise the current understanding of pikeperch spawning phenology in the temperate zone.
Open AccessHatched Late to Be Fed? Identifying the Origin of Late-Summer Pikeperch Cohorts Using Daily Otolith Increments
Effective fisheries management depends on a clear understanding of the recruitment dynamics of young-of-year (YOY) fish. Analysis of two-decade ichthyological data from Czechia and the Netherlands revealed an unexpectedly small cohort of YOY pikeperch (Sander lucioperca) in late summer. The origin of these individuals remained speculative. Building on the long-term patterns documented in these regions, we provide a new empirical contribution by analyzing the daily otolith increments of 29 pikeperch individuals sampled in the Lipno Reservoir (Czechia) in late August 2023. The otolith-based aging revealed that the extremely small pikeperch were not more than 35 days old, indicating they hatched at the turn of July and August. Even with the uncertainty in the exact timing of the first otolith increment formation, this approach disclosed the origin of the extremely small cohort as late-hatched individuals produced by wild late-spawning pikeperch. These extremely small, delayed pikeperch coexist with their normal, earlier-spawned conspecifics, which are often already piscivorous. Although they mostly do not survive the first winter, they still contribute to the recruitment indirectly by serving as prey for conspecifics. Our results highlight the need to revise the current understanding of pikeperch spawning phenology in the temperate zone.
- Open Access
Hypolimnetic Aeration Versus Predatory Fish Stocking to Address Water Quality Parameters: A Case Study from Four Czech Reservoirs
Limnological parameters were monitored in four highland reservoirs in the Czech Republic from 2022 to 2024 to evaluate the effects of management practices on water quality. Although the reservoirs share similar morphometry and all serve as drinking water sources, they differ in trophic status and management: Hubenov (HU, eutrophic) is stocked with piscivores, Nová Říše (NŘ, mesotrophic) undergoes hypolimnetic aeration, and Landštejn (LA, meso-oligotrophic) and Mostiště (MO, eutrophic) receive no targeted management interventions. Limnological data were collected monthly from April to October along vertical profiles in dam parts of the reservoirs. Comparisons were performed using graphical presentation and linear mixed-effects models. Analyses of abiotic (thermal, oxygen, and pH stratification, transparency, total phosphorus (TP) and nitrogen (TN) concentrations) and biotic (algae chlorophyll-a, cyanobacterial pigments, zooplankton density and composition) variables revealed that HU and MO exhibited the lowest transparency (on average 1.9 m in both in contrast to 2.2 m and 2.8 m in NŘ and LA, respectively) and highest seasonal algae chlorophyll-a concentrations (11.4 µg/L in HU and 15.1 µg/L in MO in contrast to 6.4 µg/L in NŘ and 5.5 µg/L in LA), indicating negligible improvement from biomanipulation. In contrast, NŘ demonstrated nutrient and chlorophyll-a levels comparable to LA (TP: 0.010 mg/L and 0.009 mg/L, TN: 1.591 mg/L and 0.419 mg/L, in NŘ and LA, respectively), despite higher nutrient input, and achieved the second highest transparency. Zooplankton densities were similar across reservoirs, supporting the hypothesis of bottom-up control or insufficient piscivore impact. These findings highlight the importance of reducing nutrient inputs to preserve water quality. Hypolimnetic aeration, which enhances sediment nutrient retention, appears more effective at mitigating eutrophication and controlling algal proliferation than fish stocking, a commonly applied biomanipulation approach.
Open AccessHypolimnetic Aeration Versus Predatory Fish Stocking to Address Water Quality Parameters: A Case Study from Four Czech Reservoirs
Limnological parameters were monitored in four highland reservoirs in the Czech Republic from 2022 to 2024 to evaluate the effects of management practices on water quality. Although the reservoirs share similar morphometry and all serve as drinking water sources, they differ in trophic status and management: Hubenov (HU, eutrophic) is stocked with piscivores, Nová Říše (NŘ, mesotrophic) undergoes hypolimnetic aeration, and Landštejn (LA, meso-oligotrophic) and Mostiště (MO, eutrophic) receive no targeted management interventions. Limnological data were collected monthly from April to October along vertical profiles in dam parts of the reservoirs. Comparisons were performed using graphical presentation and linear mixed-effects models. Analyses of abiotic (thermal, oxygen, and pH stratification, transparency, total phosphorus (TP) and nitrogen (TN) concentrations) and biotic (algae chlorophyll-a, cyanobacterial pigments, zooplankton density and composition) variables revealed that HU and MO exhibited the lowest transparency (on average 1.9 m in both in contrast to 2.2 m and 2.8 m in NŘ and LA, respectively) and highest seasonal algae chlorophyll-a concentrations (11.4 µg/L in HU and 15.1 µg/L in MO in contrast to 6.4 µg/L in NŘ and 5.5 µg/L in LA), indicating negligible improvement from biomanipulation. In contrast, NŘ demonstrated nutrient and chlorophyll-a levels comparable to LA (TP: 0.010 mg/L and 0.009 mg/L, TN: 1.591 mg/L and 0.419 mg/L, in NŘ and LA, respectively), despite higher nutrient input, and achieved the second highest transparency. Zooplankton densities were similar across reservoirs, supporting the hypothesis of bottom-up control or insufficient piscivore impact. These findings highlight the importance of reducing nutrient inputs to preserve water quality. Hypolimnetic aeration, which enhances sediment nutrient retention, appears more effective at mitigating eutrophication and controlling algal proliferation than fish stocking, a commonly applied biomanipulation approach.
- Open Access
- 12 February 2025
- Published by Wiley in Journal of Fish Biology
- Vol. 106 (6) , 1893-1898
Pelagic distribution and night foraging of early juvenile European catfish ( Silurus glanis L .)
This study provides evidence of pelagic occurrence and night feeding in early juvenile European catfish that contributed 0.2% to the early juvenile pelagic community at night in Klíčava, 0.3% in Římov, and 3.3% in Žlutice Reservoirs in the Czech Republic. The catfish occurred mostly at a depth of 2–4 m. Their abundance was 5.5 inds.1000 m −3 in Klíčava Reservoir (2018), 0.3 inds.1000 m −3 in Římov Reservoir (2018), and 88.8 inds.1000 m −3 in Žlutice Reservoir (2019). Catfish fed on phantom midges ( Chaoborus sp.).
- 12 February 2025
- Published by Wiley in Journal of Fish Biology
- Vol. 106 (6) , 1893-1898
Open AccessPelagic distribution and night foraging of early juvenile European catfish ( Silurus glanis L .)
This study provides evidence of pelagic occurrence and night feeding in early juvenile European catfish that contributed 0.2% to the early juvenile pelagic community at night in Klíčava, 0.3% in Římov, and 3.3% in Žlutice Reservoirs in the Czech Republic. The catfish occurred mostly at a depth of 2–4 m. Their abundance was 5.5 inds.1000 m −3 in Klíčava Reservoir (2018), 0.3 inds.1000 m −3 in Římov Reservoir (2018), and 88.8 inds.1000 m −3 in Žlutice Reservoir (2019). Catfish fed on phantom midges ( Chaoborus sp.).
- 2 July 2024
- Published by Taylor & Francis in Lake and Reservoir Management
- Vol. 40 (3) , 317-329
Fish predation on newly stocked juvenile predatory fish in a biomanipulated reservoir
- 2 July 2024
- Published by Taylor & Francis in Lake and Reservoir Management
- Vol. 40 (3) , 317-329
Fish predation on newly stocked juvenile predatory fish in a biomanipulated reservoir
- Open Access
Trophic Position of the Species and Site Trophic State Affect Diet Niche and Individual Specialization: From Apex Predator to Herbivore
Intra-species variability in isotopic niches, specifically isotopic total niche width (ITNW), isotopic individual niche width (IINW), and isotopic individual specialization (IIS), was studied using an innovative approach without sacrificing the vertebrates. Stable isotopes (δ13C, δ15N) in four body tissues differing in isotopic half-life were analyzed from four freshwater fish species representing different trophic positions. ITNW was widest for the apex predator (European catfish) and narrowest for the obligate predator (Northern pike). IINW exhibited a polynomial trend for the European catfish, Northern pike, and Eurasian perch (mesopredator), decreasing with body mass and increasing again after exceeding a certain species-dependent body mass threshold. Thus, for ectotherms, apex predator status is linked rather to its size than to the species. In herbivores (rudd), IINW increased with body mass. The IIS of predators negatively correlated with site trophic state. Therefore, eutrophication can significantly change the foraging behavior of certain species. We assume that the observed trends will occur in other species at similar trophic positions in either aquatic or terrestrial systems. For confirmation, we recommend conducting a similar study on other species in different habitats.
Open AccessTrophic Position of the Species and Site Trophic State Affect Diet Niche and Individual Specialization: From Apex Predator to Herbivore
Intra-species variability in isotopic niches, specifically isotopic total niche width (ITNW), isotopic individual niche width (IINW), and isotopic individual specialization (IIS), was studied using an innovative approach without sacrificing the vertebrates. Stable isotopes (δ13C, δ15N) in four body tissues differing in isotopic half-life were analyzed from four freshwater fish species representing different trophic positions. ITNW was widest for the apex predator (European catfish) and narrowest for the obligate predator (Northern pike). IINW exhibited a polynomial trend for the European catfish, Northern pike, and Eurasian perch (mesopredator), decreasing with body mass and increasing again after exceeding a certain species-dependent body mass threshold. Thus, for ectotherms, apex predator status is linked rather to its size than to the species. In herbivores (rudd), IINW increased with body mass. The IIS of predators negatively correlated with site trophic state. Therefore, eutrophication can significantly change the foraging behavior of certain species. We assume that the observed trends will occur in other species at similar trophic positions in either aquatic or terrestrial systems. For confirmation, we recommend conducting a similar study on other species in different habitats.
- Open Access
- 16 July 2023
- Published by Wiley in Ecology of Freshwater Fish
- Vol. 32 (4) , 783-794
The effect of littoral complexity on the diel distribution of early juvenile fish communities in temperate freshwater reservoirs
The diel distribution of early juvenile fish communities from two temperate freshwater reservoirs that differed in cover of submerged aquatic vegetation was investigated. In the daytime, about 99.9% of the juvenile fish community from the plant‐rich Žlutice Reservoir was found in the nearshore belt of submerged aquatic vegetation reaching an average abundance of ~7982 inds. 1000 m−3. In contrast, in the pelagic habitat, few fish were found at day. In the plant‐poor Římov Reservoir, 98.9% of juveniles occupied the pelagic habitat during daytime and reached an average abundance of ~333 inds. 1000 m−3. Vertical distribution of fish in the pelagic habitat in both water bodies was affected by steep thermal and oxygen stratification and no individuals occurred below 6 m depth. At night, 88.8% of the juvenile fish community from the plant‐rich Žlutice Reservoir was in the pelagic habitat with an average abundance of ~1423 inds. 1000 m−3. Their diel horizontal shifts were much more pronounced compared to the community from the Římov Reservoir that reached an average nighttime pelagic abundance of ~523 inds. 1000 m−3. Only 1.1% of the juvenile fish community in the Římov Reservoir was found in the littoral during the daytime and 0.7% at night reaching an average daytime abundance of ~1688 inds. 1000 m−3 and average nighttime time abundance of ~1664 inds. 1000 m−3. This study indicates that if a well‐developed littoral zone with abundant aquatic vegetation is present, early juvenile fish will perform diel horizontal movement in temperate stratified reservoirs.
- 16 July 2023
- Published by Wiley in Ecology of Freshwater Fish
- Vol. 32 (4) , 783-794
Open AccessThe effect of littoral complexity on the diel distribution of early juvenile fish communities in temperate freshwater reservoirs
The diel distribution of early juvenile fish communities from two temperate freshwater reservoirs that differed in cover of submerged aquatic vegetation was investigated. In the daytime, about 99.9% of the juvenile fish community from the plant‐rich Žlutice Reservoir was found in the nearshore belt of submerged aquatic vegetation reaching an average abundance of ~7982 inds. 1000 m−3. In contrast, in the pelagic habitat, few fish were found at day. In the plant‐poor Římov Reservoir, 98.9% of juveniles occupied the pelagic habitat during daytime and reached an average abundance of ~333 inds. 1000 m−3. Vertical distribution of fish in the pelagic habitat in both water bodies was affected by steep thermal and oxygen stratification and no individuals occurred below 6 m depth. At night, 88.8% of the juvenile fish community from the plant‐rich Žlutice Reservoir was in the pelagic habitat with an average abundance of ~1423 inds. 1000 m−3. Their diel horizontal shifts were much more pronounced compared to the community from the Římov Reservoir that reached an average nighttime pelagic abundance of ~523 inds. 1000 m−3. Only 1.1% of the juvenile fish community in the Římov Reservoir was found in the littoral during the daytime and 0.7% at night reaching an average daytime abundance of ~1688 inds. 1000 m−3 and average nighttime time abundance of ~1664 inds. 1000 m−3. This study indicates that if a well‐developed littoral zone with abundant aquatic vegetation is present, early juvenile fish will perform diel horizontal movement in temperate stratified reservoirs.
- Open Access
- 30 May 2023
- Published by Elsevier in Ecological Indicators
- Vol. 153, 110425
Calibration of fish biomass estimates from gillnets: Step towards broader application of gillnet data
- 30 May 2023
- Published by Elsevier in Ecological Indicators
- Vol. 153, 110425
Open AccessCalibration of fish biomass estimates from gillnets: Step towards broader application of gillnet data
- Open Access
- 27 March 2023
- Published by Wiley in Ecology of Freshwater Fish
- Vol. 32 (4) , 724-734
Distribution patterns, annual density changes, growth and mortality of pikeperch [Sander lucioperca (L. 1758)] fry following oligotrophication of a reservoir
Until 2006, the Lipno Reservoir had the largest catches of pikeperch in the Czech Republic, but since 2007 it has partially collapsed. This collapse was preceded by oligotrophication, when phosphorus concentrations declined by 25%. Conservation measures from 2009 to 2015 partially improved the population from 2015, but pikeperch biomass did not reach previous levels. Unsuccessful spawning and low survival of pikeperch fry were suspected as possible reasons. Pelagic trawling for pikeperch younger juveniles in June and older juveniles in August indicated that extreme mortality in the first year of life, rather than limited spawning, was the reason for low pikeperch recruitment. Large interannual differences in pikeperch density were observed in both spring and summer, and the growth was generally low. Pikeperch fry density changed over a trophic gradient with the highest densities in the eutrophic upper reservoir parts, while differences between depths were much less pronounced due to the lack of temperature and oxygen depth stratification in summer. Oligotrophication of the reservoir in recent years is probably partly responsible for the high mortality and slow growth of pikeperch fry that are still zooplanktivorous, resulting in a lower probability of surviving their first winter. Given the changing conditions in the reservoir, measures should be taken to strictly conserve populations to maintain self‐sustaining pikeperch populations in the Lipno Reservoir.
- 27 March 2023
- Published by Wiley in Ecology of Freshwater Fish
- Vol. 32 (4) , 724-734
Open AccessDistribution patterns, annual density changes, growth and mortality of pikeperch [Sander lucioperca (L. 1758)] fry following oligotrophication of a reservoir
Until 2006, the Lipno Reservoir had the largest catches of pikeperch in the Czech Republic, but since 2007 it has partially collapsed. This collapse was preceded by oligotrophication, when phosphorus concentrations declined by 25%. Conservation measures from 2009 to 2015 partially improved the population from 2015, but pikeperch biomass did not reach previous levels. Unsuccessful spawning and low survival of pikeperch fry were suspected as possible reasons. Pelagic trawling for pikeperch younger juveniles in June and older juveniles in August indicated that extreme mortality in the first year of life, rather than limited spawning, was the reason for low pikeperch recruitment. Large interannual differences in pikeperch density were observed in both spring and summer, and the growth was generally low. Pikeperch fry density changed over a trophic gradient with the highest densities in the eutrophic upper reservoir parts, while differences between depths were much less pronounced due to the lack of temperature and oxygen depth stratification in summer. Oligotrophication of the reservoir in recent years is probably partly responsible for the high mortality and slow growth of pikeperch fry that are still zooplanktivorous, resulting in a lower probability of surviving their first winter. Given the changing conditions in the reservoir, measures should be taken to strictly conserve populations to maintain self‐sustaining pikeperch populations in the Lipno Reservoir.
- Open Access
Openness of Fish Habitat Matters: Lake Pelagic Fish Community Starts Very Close to the Shore
Fish communities differ significantly between the littoral and the pelagic habitats. This paper attempts to define the shift in communities between the two habitats based on the European standard gillnet catch. We sampled the benthic and pelagic habitats from shore to shore in Lake Most and Římov Reservoir (Czech Republic). The 3 m deep pelagic nets were spanned across the water body at equal distances from two boundary points, where the depth was 3.5 m. The benthic community contained more fish, more species, and smaller individuals. The mild sloped littoral with a soft bottom attracted more fish than the sloping bank with a hard bottom and less benthos and large Daphnia. The catch of the pelagic nets was dominated by eurytopic fish—rudd (Scardinius erythrophthalmus) and roach (Rutilus rutilus) in Most and bleak (Alburnus alburnus) in Římov. With the exception of one case where overgrown macrophytes extended the structured habitat, the largest shift from the benthic to the pelagic community was observed only in the first pelagic gillnet above the bottom depth of 3.5 m. Open water catches were relatively constant with small signs of decline towards the middle of the lake. The results indicate that the benthic gillnet catch is representative of a very limited area and volume, while most of the volume is dominated by the pelagic community. This has important consequences for the assessment of the community parameters of the whole lake following the European standards for gillnet sampling design.
Open AccessOpenness of Fish Habitat Matters: Lake Pelagic Fish Community Starts Very Close to the Shore
Fish communities differ significantly between the littoral and the pelagic habitats. This paper attempts to define the shift in communities between the two habitats based on the European standard gillnet catch. We sampled the benthic and pelagic habitats from shore to shore in Lake Most and Římov Reservoir (Czech Republic). The 3 m deep pelagic nets were spanned across the water body at equal distances from two boundary points, where the depth was 3.5 m. The benthic community contained more fish, more species, and smaller individuals. The mild sloped littoral with a soft bottom attracted more fish than the sloping bank with a hard bottom and less benthos and large Daphnia. The catch of the pelagic nets was dominated by eurytopic fish—rudd (Scardinius erythrophthalmus) and roach (Rutilus rutilus) in Most and bleak (Alburnus alburnus) in Římov. With the exception of one case where overgrown macrophytes extended the structured habitat, the largest shift from the benthic to the pelagic community was observed only in the first pelagic gillnet above the bottom depth of 3.5 m. Open water catches were relatively constant with small signs of decline towards the middle of the lake. The results indicate that the benthic gillnet catch is representative of a very limited area and volume, while most of the volume is dominated by the pelagic community. This has important consequences for the assessment of the community parameters of the whole lake following the European standards for gillnet sampling design.