Knowledge of trophic structure is important to understand sources and pathways of energy resources in community ecology and to identify determinants of ecosystem changes. Yet, little is known from rivers of African savanna receiving large inputs of terrestrial organic matter and nutrients by large mammalian herbivores. We used Stable Isotope (δ¹³C and δ¹⁵N) Bayesian Ellipses in R (SIBER) and Layman's community-wide metrics to describe seasonal variation in trophic niches and trophic structures in midorder river reaches in the Mara River (Kenya) that differed in environmental conditions (agricultural vs. forested) and amounts of organic matter and nutrients (low vs. high inputs by livestock and hippopotami, Hippopotamus amphibius). These analyses were supplemented with data on the trophic diversity of macroinvertebrate functional feeding groups (FFGs) and fish trophic guilds. The δ¹³C and δ¹⁵N of basal resources and consumers differed between sites and changed with seasons. Sites in agricultural areas that were utilised by livestock and a site with hippopotami had higher δ¹³C than the forested site due to the presence of C4 carbon from egestion and excretion by the grazers. The forested site recorded the most taxon-rich and trophic-diverse invertebrate community, suggesting both autochthonous and allochthonous sources of energy were available. Agricultural sites and the site with hippopotami recorded high abundances of collector taxa in response to large inputs of organic matter. Fish trophic guilds were less diverse and were dominated by insectivores. The food web at the forested site had the widest trophic niche size and highest isotopic trophic diversity compared to sites in areas with large mammalian herbivores. Invertebrate and fish trophic niche sizes changed according to food resources varying with space and time. Invertebrates had higher δ¹³C values during the dry season. In contrast, fish showed higher δ¹³C values during the wet season, and trophic niche sizes were constricted and considerably overlapping, suggesting feeding on a narrow range of food sources with high trophic redundancy. This study showed that increased terrestrial organic matter by large mammalian herbivores affected trophic diversity and niche sizes for aquatic consumers in rivers draining the African savanna. Linking the density of terrestrial large mammalian herbivores to aquatic ecosystem structure and function could help manage their populations sustainably.