The intensification of human activities all around the globe has led to the spread of micropollutants in high-mountain freshwater environments. We therefore aimed to assess the geospatial distribution and determine the potential sources of (total-) mercury (THg) and microplastics (MPs) in mountain freshwater ecosystems. To do so, we analyzed THg and MP concentrations in brown trout, biofilm, and sediments from lotic and lentic ecosystems in the Pyrenees – all subjected to different types of human pressure. Additionally, we assessed the potential impacts of these pollutants on fish, and explored the bioindication capacity of brown trout (Salmo trutta fario) and biofilm regarding THg and MP pollution. For the first time, we measured concentrations of MPs trapped in the matrix of freshwater biofilm. Our results suggest that THg in the Pyrenees might be explained by both legacy (regional) and distant sources, in combination with environmental characteristics such as the presence of peatlands or streamwater physicochemistry, while MPs in fish are linked to recent local pollution sources such as single-use plastics. In contrast, MPs in biofilm matrix and sediments indicate a combination of distant (i.e., atmospheric deposition) and recent local pollution sources. Moreover, hydrodynamics and plastic density likely control MP distribution in rivers. Based on Fulton's condition factor, we also found that higher THg concentrations caused a negative impact on fish health (K < 1), while no impact of MPs could be seen. Therefore, we suggest that brown trout and biofilm can serve as bioindicators of atmospheric deposition of THg in high-altitude lakes and that biofilm is a reliable bioindicator to assess MP pollution in remote environments. Brown trout may also act as a bioindicator of MP pollution, but only efficiently in more polluted areas.