Intensive recirculating aquaculture relies on biofilters to sustain satisfactory water quality in the ponds. Establishment of new biofilters in aquaculture ponds without a start-up culture requires a long period of time and may therefore cause significant losses and environmental harm due to discharge of nitrogen-rich effluents. A laboratory scale setup (7-l aquaria with shrimp and fish) demonstrated that an external start-up nitrifying enrichment culture performed similarly to the natural bacterial population of an established pond biofilter, and superior to the performance of similar biofilters without a start-up culture (control). Ammonia concentration in the control treatment increased daily and reached 18 mg l−1 during a 14-day experiment, whereas in the treated aquaria, it averaged less than 2 mg l−1. Fish growth and survival were similar in the treated aquaria (average growth of 0.45 g/14 days, and 95% survival) and significantly higher than in the control (average growth of 0.0 g/14 days, and 80% survival). The source for the enrichment cultures was soil samples collected from the region where the farm is situated. This approach may lead to the development of bacterial amendments (probiotic products) that can be used as start-up cultures for new operations or damaged filters, and potentially enhance nitrification in established filters. As the cultures are collected from soils, it is unlikely that they will be contaminated with fish disease-causing agents. This will improve water quality and consequently aquatic animal production.