With rapid urbanization in China, anthropogenic reactive nitrogen (Nr) releases to urban environment contribute to water resource depletion and serious water quality deterioration. This study assessed nitrogen-related water pollution in an urbanized city (Shenzhen, China) by using the indicators of gray water footprint (GWF) and water pollution level (WPL), concerning potential impacts of aquatic Nr releases on administrate districts and affiliated urban rivers within city. The results showed that urban aquatic Nr releases decreased dynamically with average 15.98 thousand t N during 2001–2016, accompanied with the reduction in gray water footprint from 23.06 × 108 to 15.56 × 108 m3, mainly from residential activities. Administrative districts of Baoan and Longgang were the main regional GWF producers during 2012–2016. Areas containing urban rivers with especially high potential WPLs were mainly located in northern Baoan, and northeast Longgang district, and the risks for water pollution development still spread over urban water networks in Shenzhen City. Several strategies (encourage sustainable lifestyle, target infrastructure improvements and develop district-level GWF reduction targets) are needed to mitigate urban water pollution. This study provides insights into the status of assimilation capacity within a city to mitigate aquatic N pollution, meeting current water challenge.