The stretch from the riparian zone of a major river, through the mouth and upstream in tributaries forms a range of differing habitats. The aim of this study was to investigate the effect of these different habitats on the riparian frog community in primary rain forest in Borneo; i.e. examine whether any gradients could be demonstrated in terms of species composition, diversity and density of frogs, as well as which environmental characteristics that seem to be of most importance in forming habitats of high conservational value. A major river, Segama, and three of its tributaries were investigated. The surveys were carried out at night by searching for frogs visually and acoustically along the streams, from the shore of the Segama river and 400 metres upstream in the tributaries. In all transects 10 habitat variables were also measured. The results from the study show a significantly lower diversity and abundance of frogs along the shores of Segama and close to the mouths of the tributaries compared to further upstream, and a significant difference in species assemblage. Most species exhibited a negative correlation with the downstream transects or were not found there at all. The habitat characteristics waterfalls and boulders were found to be of most importance for the diversity and abundance of frogs, making these characteristics key components of habitats with high conservational value. Major rivers could also potentially form dispersal corridors for invasive species, which findings of the introduced species Fejervarya limnocharis along the shores of Segama shows.