The use of probiotics within shrimp farms has increased as an alternative to antibiotic use because of an increasing demand for more environment-friendly aquaculture. This has improved growth performance and health of shrimp, and improved pathogen control as well as water and soil quality in culture systems. However, efficacy of probiotics in intensive systems using biofloc remains uncertain. Here, bioremediation and biocontrol of a commercial probiotic was investigated through analysis of water quality and main bacterial groups that influence a Litopenaeus vannamei culture using biofloc. Furthermore, additional knowledge was gained on phytoplankton and shrimp performance. Treatments consisted of four different probiotic concentrations (Bacillus subtilis and B. licheniformis): 0.5 g m-3 (P0.5), 1 g m-3 (P1.0), 2 g m-3 (P2.0), 3 g m-3 (P3.0), and a control without probiotic (CTL). All variables were shown to be balanced and within the recommended limits for shrimp farming. Under the culture conditions adopted in this study, the commercial probiotic did not result in a significant effect (P ≥ 0.05) on water quality, bacteria, phytoplankton, or shrimp performance. Bacteria naturally present in biofloc were sufficient for maintaining the balance of culture and continued to exert excellent bioremediation and biocontrol when management was conducted properly.