Field studies were performed in stratified Lake Oglethorpe to isolate and identify culturable, free‐living bacterioplankton from lake water and those associated within zooplankton. Heterotrophic colony counts of whole water were lower than acridine orange epifluorescent direct counts by 3–4 orders of magnitude, whereas colony counts were increased by an order of magnitude when the lake water was fractionated for zooplankton, then treated and sonicated to release bacteria from within zooplankton. Cultured bacterial species were segregated by sampling depth among the epilimnion, metalimnion, and hypolimnion and the zooplankton fractions. Laboratory feeding experiments with Daphnia ambigua and mixed suspensions of these lake bacteria demonstrated that zooplankton‐associated bacteria survived induced gut retention in D. ambigua for 23 h longer than free‐living bacteria. Feeding rate experiments showed no difference between ingestion or clearance rates of the mixed cultured bacteria, but bacterial inhibition studies showed that survivors inhibited nonsurvivors. These studies suggest that some bacterioplankton can survive digestion and interact in guts of zooplankton.