The introduction of omnivorous tilapia into a variety of aquatic systems worldwide has led to a number of serious ecological problems. One of the main issues is an increase in water turbidity, which affects not only light penetration but also primary production and the distribution of phytoplankton and benthic algae in shallow lakes. These changes cause deterioration of water quality in these lakes. A 12-week mesocosm experiment was set up to test the hypotheses that omnivorous Nile tilapia (Oreochromis niloticus) introduced to a shallow water system will increase turbidity and nutrient levels in the water column and thereby boost growth of phytoplankton and depress benthic algae. Relative to the control treatments, the presence of tilapia led to higher concentrations of total nitrogen and total phosphorus in the water column, greater biomass of phytoplankton as measured by chlorophyll a (Chl a), greater concentrations of total suspended solids and inorganic suspended solids, lower light intensity, and lower biomass of benthic algae at the sediment surface. A tube-microcosm experiment using 32P radio tracer indicated that the presence of tilapia accelerated the release of sediment phosphorus (P) into the water column. We conclude that these invasive omnivorous fish not only stimulate growth of phytoplankton in shallow lakes by increasing nutrients in water column, but also depress benthic algal growth by promoting sediment resuspension, leading to increased turbidity of the water. Thus the removal of tilapia could be a useful practice for managers of shallow aquatic ecosystems, promoting benthic primary production and improving water clarity.