Aim Limnological conditions, phytoplankton and zooplankton communities in a fishpond highly affected by management during the dry and rainy seasons are investigated. Methods Water samples were analyzed for physicochemical parameters; soil samples were analyzed for macro- and micro-nutrients, phytoplankton and zooplankton communities, at four sites, during eight months in the rainy and dry seasons. Distance-based linear model (DISTLM) was applied with Akaike Information Criterion (AIC), where the influence of environmental variables in the variation of phytoplankton and zooplankton composition could be assessed and the best model could be selected. Results The multiparameter test revealed that variables pH, TSS and TP better explain the composition of the biotic community (AICc = 45.6; R2 = 0.80). Chlorophyceae was the dominant group with 32 taxa, or rather, 75-85% of total phytoplankton, with high density at 2,365-4,180 ind.L-1 during the sampling period. Rotifera was the most abundant group in the zooplankton community during the two seasons, except at IW2 during the dry season, when Copepoda had a higher density, namely, 52% of total zooplankton community at this site. Conclusions The contribution of allochthonous material to the fishpond during the two seasons mainly consists of macro- and micro-nutrients and thermotolerant coliforms that influenced the plankton community and enhanced high Cyanobacteria density in the rainy season. Plankton community in the studied pond was characteristic of small water bodies. Management protocol in places with continuous water flow according to the region may be an important tool to optimize and to avoid risks in fish production.