Shrimp is the most important aquaculture industry. Therefore, we determined the effect of nitrifying-probiotic bacteria on water quality, growth, survival, immune response and intestinal microbiota of Litopenaeus vannamei cultured without water exchange. In vitro, only B. licheniformis used TAN, nitrites and nitrates since nitrogen bubbles were produced. TAN decreased significantly in the treatments with bacilli and LAB, but no differences were observed in nitrites. Nitrates were significantly higher in the treatments with bacteria. The final weight and survival of shrimp in the bacterial treatments increased significantly and superoxide anion increased significantly only in LAB treatment. The activity of phenoloxidase decreased significantly in the treatment with LAB and with the mixture of bacilli and LAB. Shrimp treated with bacilli in the water showed lower species richness. The gut bacterial community after treatments was significantly different from that of the control. Linoleic acid metabolism was positively correlated with final weight and superoxide anion, whereas quorum sensing was correlated with survival. Thus, bacilli and LAB in the water of hyperintensive culture systems act as nitrifers, modulate the intestinal microbiota and immune response, and improve the growth and survival of shrimp. This is the first report on Pediococcus pentosaceus and Leuconostoc mesenteroides as nitrifying bacteria.