Long-term plankton studies in neotropical lakes are scarce. Here we studied plankton composition in Lake Cote, Costa Rica, twice per year from 2002 to 2018, to monitor changes after it was modified as a reservoir for hydroelectricity in 2003. Plankton variation was examined for a long-term trend and its relationship with basic limnological characteristics of the lake. Phytoplankton was sampled from the surface and with a depth-integrating sampler. Zooplankton was caught with vertical hauls, at the same station at the middle of the lake. A total of 138 taxa of microalgae occurred, most from Chlorophyta and Cyanobacteria, to which dominant species belonged; Aulacoseira granulata was also ubiquitous. A shift in dominance occurred, from Cosmarium asphaerosporum to Aphanothece cf. microscopica, and Aphanocapsa cf. delicatissima. Zooplankton included 23 species of Cladocera, Copepoda, Rotifera, and Chaoborus. Most abundant were Keratella americana, Eubosmina tubicen, and Cyclopoida; Daphnia laevis became abundant after 2007 while E. tubicen declined. There was little correspondence between both planktonic components. Plankton composition was typical of a mesotrophic to eutrophic shallow lake, but changes indicated an increase in stratification, and can be attributed to combined effects of recent warming and outflow management for hydropower production.