Rivers are important sources of water and energy to the people and growing economies of Africa, but they are also vibrant and biologically diverse ecosystems in their own right. Human use invariably exerts negative pressures on riverine ecosystems, including alteration of natural flow regimes due mainly to flow regulation by dams and water abstractions. Severe alteration of natural flow regimes changes the physicochemical environment of rivers and reduces the abundance, diversity and specific characteristics of habitats used by native aquatic and riparian species, leading to unacceptable declines in ecosystem condition. In order to minimize the impacts of flow alterations and maintain acceptable ecosystem conditions, water managers are expected to maintain an environmental flow regime in rivers. African rivers exhibit a wide variety of flow regimes to which riverine species have adapted their life histories. Research over recent decades has identified important flow-ecology relationships that have been used to quantify environmental flow requirements in many river systems, and environmental flow requirements have been incorporated into the management actions of some rivers. However, the assessment and implementation of environmental flows have been highly variable across the continent, and additional effort is needed to protect environmental flows in all African rivers. This chapter explores some of the key aspects of environmental flow science and practice in Africa, both today and looking into the future.

Knowledge of the trophic structure and the major energy sources supporting metazoan production are important considerations for biodiversity conservation and ecosystem management. African streams and rivers face multiple stressors from agricultural intensification, deforestation, and municipal and industrial effluents coupled with uncontrolled water abstractions. Yet, the effects of these influences on ecosystem structure and functioning are poorly understood. In this chapter, we review the trophic dynamics of African riverine ecosystems with a focus on trophic structure, the major sources of energy supporting food webs, and the influence of human activities. While much of the data used for this review are from African studies, we also reference other studies in the tropics for comparison and to fill existing knowledge gaps. Based on available information, autochthony, short food chains, and an increased tendency toward omnivory characterize food webs in African streams and rivers. However, trophic interactions and dynamics in these systems are witnessing changes caused by human activities. Changes in trophic diversity and dynamics include shifts from allochthony to autochthony following the deforestation of forested headwater streams, top-down control of local fish and invertebrate populations caused by introduced predatory fish such as trout, and shrinkage of trophic niche sizes caused by land use change. Despite these developments, studies on food web structure and trophic dynamics are very limited in low-order streams, and we have identified future research needs that need to be addressed to fill knowledge gaps that would hinder biodiversity conservation and effective management of riverine ecosystems in African rivers, including their fisheries.

Many streams and rivers outside conservation areas across the Afrotropics face multiple stressors from land use change, urbanization, and excessive water withdrawals. Thus, there is a need to develop cost-effective tools for assessing and monitoring ecological changes to inform management decisions. Studies utilizing macroinvertebrate communities as indicators of the ecological condition of streams and rivers in the Afrotropics use diverse methods, including diversity, richness, biotic and multimetric indices. However, some of these indices are region- or country-specific, which limits their general use across multiple regions or countries. In this study, we address this challenge by testing and comparing the performance of diversity and richness indices (e.g., Shannon-Wiener and Simpson), regional biotic indices (the African Scoring System Version 5 [SASS5], Tanzanian River Scoring System [TARISS] and a biotic index developed for the Ethiopian highlands [ETHbios]), and a macroinvertebrate-based index of biotic integrity (M-IBI) in assessing the ecological condition of Afrotropical rivers with the transboundary Mara River, Kenya and Tanzania, as a case study. In this study, we analyzed water and habitat quality degradation caused by multiple stressors such as land use change, organic pollution and flow alteration and the corresponding responses in macroinvertebrate communities. We utilized macroinvertebrates data collected from 143 sites covering the entire gradient of the river and its major tributaries in Kenya and Tanzania. To develop the M-IBI, we used 12 metrics that describe macroinvertebrate community richness, composition, tolerance to disturbances (indicator taxa), and the composition of functional feeding groups. Although all the biotic indices were sensitive to poor water quality and human disturbance of the river, the M-IBI performed better than biotic indices (SASS5, Tanzanian River Scoring System, and Ethiopian highlands), diversity and richness indices by having a higher discriminatory ability of site categories according to different levels and types of disturbance. Diversity and richness indices performed poorly and failed to discriminate between stressor gradients in the river. This study demonstrates a need for testing and evaluating indices or protocols before adoption and use in biomonitoring streams and rivers in other countries and regions. There is an even greater need to assess the tolerance of macroinvertebrate taxa before inclusion in biotic indices for improved performance as discriminators of multiple stressors.

Understanding the biotope requirements of the various aquatic biota is crucial for effective biomonitoring. Yet, the biotope preferences of macroinvertebrates in Afrotropical rivers have been poorly studied. In this study, we investigated the influence of human disturbance and flow-driven biotope changes on the β-diversity and biotope preferences of macroinvertebrates in the Mara River, Kenya. Macroinvertebrates were sampled from various biotopes at seven reference and nine impaired sites in wet and dry seasons. β-Diversity was determined (i) for each biotope and (ii) at the site scale, combining all biotopes sampled, and macroinvertebrate biotope preferences were assessed among biotopes between reference and impaired sites. Minor β-diversity differences were observed between reference and impaired sites based on relative abundance data, but differences were greater when the presence–absence data were used. There were no statistically significant changes in macroinvertebrate biotope preference due to human disturbance, but fidelity to preferred biotopes increased at impaired sites. In fast-flowing waters, Simuliidae, Baetidae, Tricorythidae, and Hydropsychidae dominated stable rocky substrates and were the most sensitive to flow alteration. This study adds valuable information on the effects of biotope reduction/loss and flow alteration on the diversity and biotope preferences of macroinvertebrates in Afrotropical rivers, and contributes to improvement of relevant bioassessment protocols and biodiversity conservation efforts.

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.