Total reflection X-ray fluorescence spectrometry (TXRF) is a well-accepted technique for ultra-trace analysis of ultra-pure reagents and silicon wafers. Nevertheless, the technique’s linear range is not well characterized. In this paper, the upper limits of the linear range of TXRF on micro-droplet residues are identified and the origin of the non-linear effect is investigated. It is observed experimentally that a systematic decrease in the accuracy occurs as a function of the metallic content, starting from amounts above 3–10 ng, depending on the sample composition. A mass-absorption model for thin films is re-formulated for the micro-droplet residue samples and the model parameters are tested on the experimental observations. The calculations are in good agreement with the experimental data. Finally, solutions to deal with these saturation effects are discussed and a method to extend the dynamic range of TXRF is proposed.