We examine the biodiversity and assemblage organization of freshwater fish and macroinvertebrates. Our primary model system is Lake Balaton and its catchment, which is affected by a variety of human impacts. The primary focus is to explore the environmental drivers of population dynamics and assemblage organization, and, from an applied perspective, to put forward suggestions for environmental managers and conservationists to mitigate human impacts. Specifically, we examine the habitat use, ontogenetic diet patterns, trophic relationships, growth, and survival of fish in Lake Balaton. Research on macroinvertabrates focuses especially on exploring the diversity, spatial and temporal dynamics and production of midge assemblages. The main task of the monitoring of the waterbasin’s streams is to follow the distribution of non-native invasive species and to explore their impact on the native fauna. Increasing emphasis is given to the study of the diversity and distribution of fish and macroinvertebrates in a regional (country-wide) scale to develop monitoring systems for evaluating environmental health, base conservation planning and to explore the effects of human impacts on freshwater biodiversity in the Pannon Ecoregion.