Aquatic organisms are consistently exposed to a mixture of micropollutants that can bioaccumulate, undergo biotransformation, and may exert mixture effects. However, little is known on the underlying mechanisms and species-specificity. Herein we investigated bioaccumulation, biotransformation and synergistic effects of azole (i.e., prochloraz) and strobilurin (i.e., azoxystrobin) fungicides in the two aquatic invertebrate species, Hyalella azteca and Gammarus pulex. Bioaccumulation of azoxystrobin was similar, whereas bioaccumulation of prochloraz was slightly different in the two species but was still significantly below the REACH criteria for bioaccumulative substances. Similar biotransformation patterns were observed in both species, and only a few unique biotransformation reactions were detected in H. azteca such as malonyl-glucose and taurine conjugation. Toxicokinetic modeling additionally indicated that biotransformation is a more important elimination pathway in H. azteca. In mixtures, no-observed-adverse-effect levels of prochloraz decreased the LC50s of azoxystrobin in both species which correlated well with increased internal azoxystrobin concentrations. This synergistic effect is partly due to the inhibition of cytochrome P450 monooxygenases by prochloraz which subsequently triggered the reduced biotransformation of azoxystrobin (lower by five folds in H. azteca). The largely similar responses in both species suggest that the easier-to-cultivate H. azteca is a promising representative of invertebrates for toxicity testing.