© 2019, Springer Nature Switzerland AG. Biofilm-based systems for shrimp aquaculture have emerged as a novel alternative to improve the water quality and obtain a better performance into ponds using zero or limited water exchange. The aims of this work were (1) to evaluate the production response and water quality of a super-intensive shrimp culture using a phototrophic biofilm as complementary food and (2) to study the bacterial diversity of these biofilms. A trial was performed, consisting of a shrimp culture system using biofilms as food source and a control without biofilms. Results showed that the biofilm-based system had better water quality and shrimp registered a higher growth performance compared to the control. Regarding the taxonomic profile of bacterial populations detected in the biofilm, results revealed that Proteobacteria, Bacteroidetes, and Planctomycetes were the three most abundant phyla; of these, eight bacterial orders belonging Rhizobiales, Clostridiales, Cytophagales, Actinomycetales, Vibrionales, Flavobacterales, Planctomycetales, Chlamydiales, and Rhodobacterales constituted a microbial core maintained over time. Some of these are related to anaerobic and aerobic removal processes of nitrogen. The results of this study are a first approach to understand how the bacterial communities forming biofilms are related to water quality of ponds and production performance of aquaculture farms, and how the microbial succession may cause changes on the taxonomic profile biofilms.