In this work, a novel efficient bioremediation process was established for simultaneous removing nitrate, nitrite, ferrous and manganese from water. The effects of experimental parameters (e.g., temperatures, pHs and n(NO3-N)/n(NO2--N) ratios) on the denitrification performance were investigated systematically. In the growth batch assay, the nitrate can be completely removed and the corresponding removal rate was as high as 0.2153 mg-N/(L.h). Besides, 43% of Mn(II) ions and 100% of Fe(II) ions can also be oxidized simultaneously. On the basis of Monod, Edwards, Aiba, and Luong equations, various kinetic models were established for analysis of the substrate effect on denitrification. The analysis of PCR amplification demonstrated that the nitrate reductase gene and Mn(II)-oxide gene were the napA and cumA, respectively. The results of X-ray diffractograms (XRD) indicated that Fe(II) and Mn(II) were oxidized into the corresponding oxides. Interestingly, the analysis of gas chromatography (GC) exhibited that nitrate almost turned into N-2, highlighting that the denitrifying process would not cause the greenhouse effect. Overall, the strain Pseudomonas sp. H117-based bioremediation process proposed in this work exhibited a great potential for green remediation of the polluted groundwater.