A novel marine origin Bacillus subtilis strain H1 isolated from a shrimp culture pond effectively removed NH4+‐N, NO2-‐N and NO3-‐N, with a maximum ammonium, nitrite and nitrate removal rate of 2.35 mg NH4+‐N L−1 hr−1 per OD, 9.64 mg NO2-‐N L−1 hr−1 per OD and 0.75 mg NO3-‐N L−1 hr−1 respectively. The gas chromatography–isotope ratio mass spectrometry results indicated that N2O was emitted when 15NH4Cl, Na15NO2 or Na15NO3 was used. Additionally, N2 was also produced when Na15NO2 was used. Single‐factor experiments suggested that the optimal conditions for NH4+‐N and NO2-‐N removal were glucose as a carbon source, C/N 15, initial pH 7.5, 30 g/L NaCl, 28°C and a shaking speed of 160 rpm. Orthogonal tests showed that the optimal conditions for NH4+‐N removal were C/N 15, pH 9, 10 g/L NaCl and shaking speed 160 rpm when ammonium chloride was used as the substrate. The optimal conditions for NO2-‐N removal were C/N 10, pH 6, 10 g/L NaCl and a shaking speed of 160 rpm when sodium nitrite was used as the substrate. In summary, B. subtilis strain H1 had highly efficient aerobic nitrifying–denitrifying ability and high adaptability, suggesting that it is potentially valuable to marine aquaculture.