Nile tilapia is a highly invasive fish species, deliberately introduced into many lakes and reservoirs worldwide, sometimes resulting in significant ecosystem alterations. A short-term mesocosm experiment with and without Nile tilapia (Oreochromis niloticus) was designed to test the hypotheses that the presence of tilapia may affect phytoplankton community structure, increase nutrients availability in water column and deteriorate water quality. Nutrients, total suspended solids (TSS) and biomass of phytoplankton in different size classes (as Chl a) were measured. We found that tilapia increased the total nitrogen (TN), total dissolved nitrogen (TDN), NH4
+ and TSS concentrations, deteriorating the water quality. In addition, under tilapia presence, the biomass of phytoplankton, as well as that of micro- and nano-phytoplankton, increased leading to a change in the structure of the phytoplankton assemblage. Moreover, a reduction in the biomass of periphyton was observed. Omnivorous tilapia is often dominant in tropical and subtropical waters, and removal of this fish may represent an effective management tool to improve the water quality.