Oreochromis niloticus × Oreochromis mossambicus, or red hybrid tilapia fish is the second most cultivated fish in the world due to its adaptability for fish farming, commercial viability, and reliable market values. Hence, the demand for it is high in Malaysia. Yet, concerns about heavy metal contamination in aquaculture have been widely reported from sources such as untreated residential, agricultural, and industrial effluents. This study investigates the effects of lead (Pb) and copper (Cu) on red hybrid tilapia fish on its behavioral changes and gill histology, as well as the potential mitigating effects of bioflocculant produced by Bacillus subtilis UPMB10. Seventy-two-hour toxicity tests exposed the tilapia fishes to the metals at varying concentrations with and without bioflocculants. Fish observation included mortality and behavioral changes of appetite loss, imbalance, and aggression. The results indicated that exposure to both metals led to significant behavioral changes, such as erratic swimming, increased aggression, and appetite loss with severity increasing as metal concentrations increased from 60 to 100 mg/L for Pb and 10 to 30 mg/L for Cu. Mortality rates rise with increasing metal concentrations, from 33 to 67% for Pb and 20 to 80% for Cu. Histological tests revealed that fish exposed to these pollutants had lamellae shortening and fusion in their gills, consistent with the observed stress behaviors. However, the use of bioflocculants showed positive results in reducing these impacts with fish in tanks treated with bioflocculants showed fewer severe behavioral changes (severe to moderate or no changes) and improved gill condition by about 10–20% reduction in occurrences (severe to moderate or moderate to mild effects), implying that bioflocculants can mitigate the harmful effects of heavy metals. Despite promising findings, some behavioral abnormalities and elevated Pb-related deaths were observed, likely due to protein foam formation in the tank, which reduced oxygen levels. Nonetheless, bioflocculants seem effective in lowering Pb and Cu toxicity in red hybrid tilapia, though further research is needed to confirm their efficiency across various heavy metals and fish species. This study demonstrates how bioflocculants can increase aquaculture viability in the face of environmental pollution issues.