A droplet-based microfluidic technique for testing multiple reagent concentrations is presented. We used this experimental approach to study combined effects of gold (AuNP) and silver nanoparticles (AgNP) with the phenolic uncoupler 2,4-dinitrophenol (DNP) with respect to the growth of Escherichia coli. In order to evaluate the toxicity of binary mixtures, we first encapsulated the E. coli cells and particle mixtures inside the microdroplets using PEEK (polyetherketone) modules. Two-dimensional concentration spaces with about 500 well separated droplets were addressed. We subsequently analyzed the cell growth, the viability and the autofluorescence intensity (metabolic activity) of the bacteria with a micro-flow-through fluorometer and photometer. Dose-dependent synergistic effects were found for the binary mixture of AgNPs and DNP, which indicated a stronger interaction in the mixture than it was expected from effect summation. For the binary mixture of DNP and AuNPs in non-toxic concentrations, we found only weak synergistic effects at low DNP concentrations. Furthermore, the non-toxic tested AuNPs causes effect summation in the binary mixture with the phenolic uncoupler. In general, we demonstrated the efficiency of a droplet-based microfluidic system for fast high-throughput screenings of binary and multiple mixtures. This work also confirmed the relevance of highly resolved droplet-based assays for the miniaturization of ecotoxicological aquatic test systems.