To properly conserve, restore and manage riverine ecosystems and the services they provide, it is pertinent to understand their functional dynamics. However, there is still a major knowledge gap concerning the functioning of tropical rivers in terms of energy sources supporting riverine fisheries. I reviewed the anthropogenic influences on organic matter processes, energy sources and attributes of riverine food webs in the Lake Victoria basin, but also expanded the review to incorporate recent research findings from the tropics. Contrasting findings have been presented on the diversity of shredders and their role in organic matter processing in tropical streams. Recent tropical research has also highlighted the importance of autochthonous carbon, even in small forested streams. However similar studies are very limited in Afrotropical streams making it difficult to determine their place in emerging patterns of carbon flow in the tropics. This study was conducted in the Mara River, which is an important transboundary river with its headwaters in the Mau Forest Complex in Kenya and draining to Lake Victoria through Tanzania. In its headwaters, the basin is drained by two main tributaries, the Amala and Nyangores Rivers which merge in the middle reaches to form the Mara River mainstem. The overall objective of this dissertation was to better understand the functioning of the Mara River by assessing the spatio-temporal dynamics of organic matter sources and supply under different land-use and flow conditions and the influence of these dynamics on energy flow for consumers in the river. I collected benthic macroinvertebrates from open- and closed-canopy streams and classified them into functional feeding groups (FFGs) using gut content analysis. In total, I identified 43 predators, 26 collectors, 19 scrapers and 19 shredders. Species richness was higher in closed-canopy forested streams where shredders were also the dominant group in terms of biomass. Seven shredder taxa occurred only in closed-canopy forested streams highlighting the importance of maintaining water and habitat quality, including the input of leaf litter of the right quality, in the studied streams. The findings suggest that Kenyan highland streams harbor a diverse shredder assemblage contrary to earlier findings that had identified a limited number of shredder taxa. I subsequently used the composition of invertebrate functional feeding groups (FFGs) and the ecosystem process of leaf breakdown as structural and functional indicators, respectively, of ecosystem health in upland Kenyan streams. Coarse- and fine-mesh litterbags were used to compare microbial (fine-mesh) with shredder + microbial (coarse-mesh) breakdown rates, and by extension, determine the role of shredders in litter processing of leaves of different tree species (native Croton macrostachyus and Syzygium cordatum and the exotic Eucalyptus globulus). Breakdown rates were generally higher in coarse- compared with fine-mesh litterbags for the native leaf species and the relative differences in breakdown rates among leaf species remained unaltered in both agriculture and forest streams. Shredders were relatively more important in forest compared with agriculture streams where microbial breakdown was more important. Moreover, shredder mediated leaf litter breakdown was dependent on leaf species, and was highest for C. macrostachyus and lowest for E. globulus, suggesting that replacement of indigenous riparian vegetation with poorer quality Eucalyptus species along streams has the potential to reduce nutrient cycling in streams. To study organic matter dynamics is these streams, I assessed the influence of land use change on the composition and concentration of dissolved organic matter (DOM) and investigated its links with whole-stream ecosystem metabolism. Optical properties of DOM indicated notable shifts in composition along a land use gradient. Forest streams were associated with higher molecular weight and terrestrially derived DOM whereas agriculture streams were associated with autochthonously produced and low molecular weight DOM and photodegradation due to the open canopy. However, aromaticity was high at all sites irrespective of catchment land use. In agricultural areas high aromaticity likely originated from farmlands where soils are mobilized during tillage and carried into streams and rivers by runoff. Gross primary production (GPP) and ecosystem respiration (ER) were generally higher in agriculture streams, because of slightly open canopy and higher nutrient concentrations. The findings of this study are important because, in addition to reinforcing the role of tropical streams and rivers in the global carbon cycle, they highlight the consequences of land use change on ecosystem functioning in a region where land use activities are poised to intensify in response to human population growth. Lastly, I used natural abundances of stable carbon (δ13C) and nitrogen (δ15N) isotopes to quantify spatial and temporal patterns of carbon flow in food webs in the longitudinal gradient of the Mara River. River reaches were selected that were under different levels of human and mammalian herbivore (livestock and wildlife) influences. Potential primary producers (terrestrial C3 and C4 producers and periphyton) and consumers (invertebrates and fish) were collected during the dry and wet seasons to represent a range of contrasting flow conditions. I used Stable Isotope Analysis in R (SIAR) Bayesian mixing model to partition terrestrial and autochthonous sources of organic carbon supporting consumer trophic groups. Overall periphyton dominated contributions to consumers during the dry season. During the wet season, however, the importance of terrestrially-derived carbon for consumers was higher with the importance of C3 producers declining with distance from the forested upper reaches as the importance of C4 producers increased in river reaches receiving livestock and hippo inputs. This study highlights the importance of large mammalian herbivores on the functioning of riverine ecosystems and the implications of their loss from savanna landscapes that currently harbour remnant populations. The results of this dissertation contribute data to discussions on the effects of land use change on the functioning of upland streams and food webs in savanna rivers with regard to carbon flow and the vectoring role played by large mammalian herbivores as they transfer terrestrial organic matter and nutrients into streams and rivers. This study also provides information and recommendations that will guide future research and management actions for the sustainability of the Mara River and linked ecosystems in the Lake Victoria basin.