As an intersection that links terrestrial and aquatic ecosystems, river ecosystems are hotspots for nitrogen (N) removal. Nitrification and denitrification processes have been recognized as the primary mechanisms behind permanent N removal in rivers, which can be influenced by a variety of environmental factors. However, in rivers characterized by low carbon to nitrogen (C/N) ratio, the interaction among environmental factors and their effects on the sediment N-removal rates remain to be elucidated. In this study, we conducted six surveys in the Chuanfang River (an urban low C/N ratio river flowing into the Dianchi Lake) to investigate the effects of four categories of environmental variables on sediment N-removal rates (water physicochemical properties, water nutrients, sediment characteristics, and submerged vegetation) and their respective contribution to sediment Nremoval rates. The results showed that sediment N-removal rates increased along the river reach, accompanied by a gradual improvement in water quality, sediment fertility, and submerged vegetation. Furthermore, comprehensive results of multiple analysis indicated positive effects of water physicochemical properties (e.g. dissolved oxygen, pH, temperature, etc.), sediment characteristics (e.g. sediment C, N, etc.), and submerged vegetation (e.g. tissue C, N, etc.) on the N-removal rates but emphasized the restriction of water nutrients (e.g. water N, etc.). In addition, the significant negative correlation between nitrification and denitrification in path model signified the decoupled nitrification–denitrification in the Chuanfang River. This study suggested that river ecosystems that received low C/N water had a great N-removal capacity, which could be further enhanced by the improvement of water quality, sediment fertility, and submerged vegetation.