Ecological processes, population dynamics and species interactions in shallow lakes and reservoirs are affected by seasonal and inter-annual fluctuations in rainfall and runoff. The present study aimed to explore the relationship between riverine runoff and phytoplankton community structure in Koka Reservoir, Ethiopia. Onsite measurements and collection of water samples and phytoplankton were performed at monthly intervals from January to August 2016 at three sampling sites along a stretch of the reservoir running from the river mouth to center and the outlet (dam). The results showed the decline in phytoplankton biomass at the river mouth site. The decline was particularly noticeable during the period of high rainfall and runoff compared to that of the low water period. This was associated with the hydrodynamics-induced high turbidity and reduced euphotic depth. Our results implied that phytoplankton community structure was strongly influenced by flood pulse. The results suggest that river flow and watershed management have the potential to be used more widely as an aquatic resources management option in small and medium-sized lakes and reservoirs.