Microplastic poses a threat for ecosystems because it interacts with organisms, however the long-term consequences are unknown. Freshwater ecosystems are considered as important in microplastics transport but are insufficiently researched. Caddisflies (Trichoptera, Insecta) are potential bioindicators for microplastics in freshwater ecosystems because they build protective cases using larval silk to glue sediment particles, plant parts, and even microplastics. The goal of this thesis is to optimise the method for extraction and quantification of microplastic particles in sediment and biogenic formations of freshwater ecosystems. I tested different methods and determined the optimal protocol for: digestion of the organic component (H2O2 treatment), separation of microplastics from the microplastic-mineral residue mixture (NaBr solution); detection of microplastic particles (staining and UV light). The protocol was then used to test incorporation of microplastics into the caddisfly protective cases and sediment from a previously conducted microcosm experiment with two treatments: microplastics and microplastics+pharmaceuticals. There were no differences in number and size of microplastics found in the sediment of different treatments. Moreover, there were no differences in microplastics incorporated into the caddisfly cases over the course of the experiment within each treatment. However, differences were found in both number and size of microplastics incorporated into the pupal cases at the end of experiment between treatments. These are most likely related to differences in adsorption, biofilm growth and sedimentation of microplastic particles. Thus, further research is needed to determine whether microplastics behave differently in the environment if found in combination with multiple stressors.