The contamination of surface water by nitrogen due to fertilizer application and discharge of wastewater is an increasingly serious problem. A multifunctional device, which combines water-lifting and aeration (WLA) with oligotrophic biological contact oxidation (OBCO), was developed for pretreatment of raw water to reduce nitrogen. The performance of nitrogen removal and changes in microbial community structure were investigated. The results showed that the combined technique of WLA-OBCO was feasible, and that ammonium, nitrate, total nitrogen and total organic carbon were effectively removed. Meanwhile, nitrite was mostly undetectable. The PCR-DGGE and clone sequencing results revealed that α-proteobacterium was the largest bacterial group, and Pseudomonas strains Y3 and J8 were the dominant bacteria.