Rates of biological invasion continue to accelerate and threaten the structure and function of ecosystems worldwide. High habitat connectivity, multiple pathways, and inadequate monitoring have rendered aquatic ecosystems vulnerable to species introductions. Past riverine invasion dynamics were largely restricted to large rivers, leaving out smaller rivers that commonly harbour high freshwater biodiversity. Moreover, biodiversity time series have rarely been used to investigate invasions across larger spatial-temporal scales, limiting our understanding of aquatic invasion dynamics. Here, we used 6067 benthic invertebrate samples from streams and small rivers from the EU Water Framework Directive monitoring program collected across Central Europe between 2000 and 2018 to assess temporal changes to benthic invertebrate communities as well as non-native species. We assessed invasion rates according to temperature, precipitation, elevation, latitude, longitude, and stream type. Overall, average daily temperatures significantly increased by 0.02 °C per annum (0.34 °C in total) while annual precipitation significantly decreased by 0.01 mm per annum (-67.8 mm over the study period), paralleled with significant increases in overall species richness (12.3 %) and abundance (14.9 %); water quality was relatively stable. Non-native species richness increased 5-fold and abundance 40-fold, indicating an ongoing community shift from native to non-native species. The observed increase in invasions was stronger in low mountain rivers compared to low mountain streams, with the share of non-native species abundance and richness declining with increasing elevation and latitude but increasing with temperature. We found thermophilic non-native species invasion success was greatest in larger sized streams, at lower latitudes, lower elevations and higher temperatures. These results indicate that widespread environmental characteristics (i.e., temperature) could heighten invasion success and confer refuge effects (i.e., elevation and latitude) in higher sites. High altitude and latitude environments should be prioritised for prevention efforts, while biosecurity and management should be improved in lowland areas subject to greater anthropogenic pressure, where non-native introductions are more likely.