River damming reduces the ecological heterogeneity of ecosystems, with a resultant shift of communities adapted to lotic conditions to those better adapted to the newly created lentic environment. Whereas the response of phytoplankton and zooplankton community composition and structure to river damming has been extensively studied in individual reservoirs, this study assessed three cascading reservoirs on the Tana River, Kenya. A total of five sampling campaigns were carried out in 2011, 2012 and 2013 for different sampling sites within each of the reservoirs, as well as upstream and downstream of the reservoirs. Plankton communities within each of the three reservoirs, and upstream of the reservoirs, were compared, indicating (i) the disappearance of 13 phytoplankton and 2 zooplankton taxa; (ii) the appearance (invasion) by 26 phytoplankton and 33 zooplankton taxa; and (iii) an opportunistic presence of 7 phytoplankton and 6 zooplankton taxa. Thirty-two genera of potentially harmful algae were also encountered, suggesting a potential future threat of harmful algal blooms. A significant reduction in phytoplankton diversity and taxa evenness was also observed, as well as increases in overall abundance in the reservoirs, compared to the river upstream of the study reservoirs. However, these ecological indices were restored to the original levels observed upstream of the study reservoirs at sites hundreds of kilometres downstream of the reservoirs.