Fluxes and composition dynamics of atmospheric nitrogen deposition play key roles in better balancing economic development and ecological environment. However, there are some knowledge gaps and difficulties in urban ecosystems, especially for small and medium-sized cities. In this study, both flux and composition (ratio of NH4+-N to NO3−-N, RN) of wet-deposited dissolved inorganic nitrogen (DIN, sum of NO3−-N and NH4+-N) were estimated and sources were identified at a long-term urban observation station in Tongling, a typical medium-sized city in eastern China during 2010–2016, respectively. Results showed that wet-deposited DIN fluxes were 33.20 and 28.15 kgN ha−1 yr−1 in Tongling city during 2010–2011 and 2015–2016, respectively. Compared to these two periods, both DIN and NO3−-N fluxes decreased by 15.2% and 31.8% for a series of NOx abatement measures applied effectively, respectively. At the same time, the NH4+-N flux remained stable and ranged from 19.53 to 20.62 kgN ha−1 yr−1, and the RN increased from 1.7 to 2.2. Seasonally, winds from the southwest and west-southwest with higher frequencies and speeds in spring and summer brought more NH4+-N and DIN wet deposition from an ammonia plant, which could threaten the safety of regional hydrosphere ecosystems. On the whole, the wet-deposited NH4+-N was threatening regional ecosystems of both the hydrosphere and forest. The wet-deposited DIN including NH4+-N in Tongling city stemmed mainly from a combined source of coal combustion and dust from Cu extraction and smelting, ammonia production, and roads. Therefore, production lines should be updated for Cu extraction and smelting industries, thermal power generations and the ammonia plant, old vehicles should be eliminated, and the use of new energy vehicles should be promoted for regional sustainable development and human health in the medium-sized city.