This study investigated the effects of fish farming on phytoplankton and zooplankton structure in a Brazilian tropical reservoir. Samplings were undertaken among 15 net cages and upstream and downstream of the cages over a 120-day period. Soon after the tilapia feeding, we observed the highest density of phytoplankton, with dominance of Cyanobacteria which probably increased due to the increase in predation pressure by cladocerans and copepods on the Cryptophyceae. However, after 30 days from that, a reduction in zooplankton density was registered due to the dominance of Cyanobacteria. The absence of a clear spatial difference in the phytoplankton and zooplankton densities was observed. The effects of the net cages on the nutrients and planktonic communities were small, probably due to the low number of net cages and fish employed, the seasons (autumn/ winter) and the hydrodynamics, as lotic traits, the strong influence of the wind, and the large extension of the mixture zone.