Experiments were conducted to test the usefulness of biofilms—a microbial consortium associated with extracellular polymeric substances attached to submersed surfaces—in reducing the levels of ammonium and phosphate of rearing system water, and as a food source for the shrimp Farfantepenaeus paulensis. A mature biofilm, which is able to keep ammonium and phosphate at low levels, occurred 10–15 days after tank cleanup, and was characterized by chlorophyll-a concentration around 5 μg/cm2. It was mainly composed of pennate diatoms (Amphora, Campylopyxis, Navicula, Sinedra, Hantschia and Cylindrotheca; ca. 9×104 cells/mg of biofilm) and filamentous cyanobacteria (Oscillatoria and Spirulina; ca. 2×105 cells/mg), though bacteria (max. 1.48×107/mg), flagellates (max. 1.08×103/mg) and ciliates (max. 3.51×102/mg) were also present. Pennate diatoms and filamentous cyanobacteria were responsible for the largest uptake of ammonium from the water, but nitrifying bacteria also played an important role. The presence of a biofilm lead to reduced exportation of phosphorus (33% less phosphate) and to a higher output of nitrate+nitrite, instead of ammonium. Biofilm was also an important complementary food source for the shrimp, increasing their growth.