Hippopotami (hippos) are ecosystem engineers that subsidize aquatic ecosystems through the transfer of organic matter and nutrients from their terrestrial grazing, with potentially profound effects on aquatic biogeochemistry. We examined the influence of hippo subsidies on biogeochemical cycling in pools of varying hydrology and intensity of hippo use in the Mara River of Kenya. We sampled upstream, downstream, and at the surface and bottom of pools of varying volume, discharge, and hippo numbers, both before and after flushing flows. The product of hippo number and water residence time served as an index of the influence of hippo subsidies (hippo subsidy index, HSI) on aquatic biogeochemistry. Low-HSI hippo pools remained oxic between flushing flows and could be a source or sink for nutrients. High-HSI hippo pools quickly became anoxic between flushing flows and exported nutrients and byproducts of anaerobic microbial metabolism, including high concentrations of total ammonia nitrogen, hydrogen sulfide, and methane. Medium-HSI hippo pools were more similar to high-HSI hippo pools but with lower concentrations of reduced substances. Episodic high discharge events flushed pools and reset them to the oxic state. Transitions from oxic to anoxic states depended on water residence time, with faster transitions to anoxia in pools experiencing smaller flushing flows. Frequent shifts between these alternative oxic and anoxic states create heterogeneity in space and time in pools as well as in downstream receiving waters. In river systems where the influence of hippos on water quality is a concern, maintaining the natural flow regime, including flushing flows, ameliorates impacts of hippos.