The nutritional quality of biofilm, a microbial community associated to an organic matrix, was evaluated in artificial substrate (polyethylene screen) in net cages during 30 days in the Patos Lagoon estuary, Southern Brazil. During this period, samples of biofilm were collected each 5 days for analysis of chlorophyll a, microorganisms abundance, dry weight, protein and lipid contents. During the study, chlorophyll a varied from 0.38 to 2.75 μg cm−2; dry weight between 7.16 and 17.63 mg cm−2; protein content from 0.43 to 1.76 mg cm−2 and lipid concentration between 1.21 and 4.23 mg cm−2. The variation of lipid in the biofilm was closely related to the abundance of free heterotrophic bacteria (34.25–56.54 × 106 cells cm−2), filamentous cyanobacteria (7.5–15.9 × 106 filaments cm−2), flagellates (6.92–12.89 × 106 cells cm−2) and mainly nematodes (29–1,414 organisms cm−2), while protein content varied similarly to the abundance of unicellular centric diatoms (52.10–179.81 × 103 cells cm−2), and nematodes. This information will allow a better management of food supply to raised aquatic organism with the utilization of natural productivity in the culture systems, with considerable decrease in production costs.