A multidisciplinary survey of three small rivers emptying to Lake Onego was carried out; information was collected regarding the aquatic biota, the species and age structure of riparian forests, their floristic diversity, and soils. The integral indicator chosen to assess the ecological condition of the watercourses was the characteristics of the rivers’ fish fauna, in particular fish of the Salmonidae family. Surveys of the rivers and riparian forest communities yielded records of 181 vascular plant species (11 of them macrophytes), 11 moss species, 2 lichen species; the fish fauna was made up of 9 species. Overall, the riparian forests featured a relatively wide range of typological diversity. The tree stands varied from the poor Ledum types (site class V) to the most productive Oxalis types (site classes III–I). Analysis of the tree species and age structure of forests in the riparian buffers revealed a prevalence of stable coniferous tree stands in good condition. Statistically reliable correlations were detected between the fish fauna and the tree species composition and inventory characteristics of the riparian forest stands, soil morphological characteristics, and the species diversity of the living ground cover and macrophytes. The species diversity of the riparian and the aquatic biotas were found to correlate positively with each other. Fish numbers were seen to negatively correlate with some characteristics of riparian forest soils (forest floor thickness, podzolic horizon), while the correlation with the humus horizon thickness was positive. Significant positive correlations were identified between aquatic organisms (fish, zoobenthos) and a majority of the stream’s hydrological parameters. The resultant up-to-date information about water-forest system components is important for understanding the role of small streams, which, alongside the scant officially recognized “spawning” rivers, are an ecological niche in the life cycle of salmonid fishes in Northwest Russia.