Pyrethroids are highly toxic towards aquatic macroinvertebrates such as Daphnia magna and can be synergized when co-occurring with azole fungicides. A sensitive analytical method for the measurement of azole-pyrethroid mixtures in aquatic macroinvertebrates is not available at present. We developed and validated an extraction, cleanup, and quantification procedure for four pyrethroid insecticides and four azole fungicides at the picograms per milligram wet weight level in D. magna using a QuEChERS approach and GC-ECD analysis. Short- and long-term matrix effects were analyzed by injection of a series of extracts from D. magna, and the best surrogate standards were identified through correlation analysis of analyte responses. The presence of matrix clearly stabilized the analyte responses (≤6% relative standard deviation of peak area compared to up to 22% when injected without matrix). The sensitivity was high with detection limits and limits of quantification between 58-168 and 119-571 pg mg(wet weight)(-1) for the azoles and 5.8-27 and 12-84 pg mg(wet weight)(-1) for the pyrethroids, respectively. Accuracy (% recovery) was between 95 and 111% and the precision (repeatability) below 10% relative standard deviation for all analytes. In the case of prochloraz, α-cypermethrin, and deltamethrin, normalization to surrogate standards led to a clear improvement of accuracy and precision by up to 8 and 4%, respectively. The method was successfully applied to the measurement of internal α-cypermethrin concentrations in D. magna under environmentally relevant exposure conditions (exposure to a pulse in the micrograms per liter range) with and without co-exposure to propiconazole.