Ammonia is the principal nitrogen waste product excreted by shrimp. Ammonia from the hemolymph (blood) of shrimp is largely excreted into the water across the gills via diffusion process in the form of un-ionized ammonia. Probiotics are increasingly used in aquaculture to control disease, improve water quality, and enhance the health status of fish and shrimp. Pro-Pond is composed of three B. subtilis strains that were selected based on their ammonia and nitrite removal capabilities under a wide range of salinities. The study evaluated the efficacy of AQUAVI® Pro-Pond on the nitrogen removal efficacy, in commercial shrimp ponds located in the Guangdong province of China. Three earthen ponds at a stocking density of ~80 shrimp/m2 were allotted to the Pro-Pond treatment. The average culture period of the three ponds lasted for 108 days (97, 112, and 115 days for the three ponds). Three other earthen ponds (average area 3,557 m2 or 5.3 mu) were assigned to commercial control and the average culture period lasted 102 days. The three ponds (average area 2,668 m2 or 4 mu) allotted for Pro-Pond group were treated with Pro-Pond at 11.3 times per pond on an average (34 times in total for the three ponds) at a dose of 0.25 ppm or 2.5 kg per ha during each application over the whole culture period (108 days). On the other hand, the three commercial control ponds were treated with four different commercial products at 10.7 times per pond on an average (32 times in total for the three ponds) over a 102-day culture period. These four commercial products were based on probiotics (Bacillus, nitrifying bacteria, Enterococcus faecalis), yeast and/or enzyme mix. Results showed that Pro-Pond was marginally better than the commercial treatment in controlling the NH3-N level (0.45 mg/l versus 0.53 mg/l; p-value = 0.10, t-test). There were no differences between the two groups on the nitrite level. Although multiple products were applied in the control ponds by the farmer, Bacillus subtilis alone was sufficient to control nitrogen waste in the commercial ponds. At the end of culture, the average harvest yield of shrimp was 505 kg/mu for the control group and 535 kg/mu for the B. subtilis group (6% higher). Results demonstrate that Bacillus subtilis based multi-strain probiotics can be effective in controlling nitrogen wastes and improving production in commercial shrimp farms