Atmospheric nitrogen deposition (AND) may lead to water acidification and eutrophication. In the five months after December 2019, China took strict isolation and COVID-19 prevention measures, thereby causing lockdowns for approximately 1.4 billion people. The Danjiangkou Reservoir refers to the water source in the middle route of South-to-North Water Diversion Project in China, where the AND has increased significantly; thus, the human activities during the COVID-19 period is a unique case to study the influence of AND to water quality. This work monitored the AND distribution around the Danjiangkou Reservoir, including agricultural, urban, traffic, yard, and forest areas. After lockdown, the DTN, DON, and Urea-N were 1.99 kg · hm−2 · month−1, 0.80 kg · hm−2 · month−1, and 0.15 kg · hm−2 · month−1, respectively. The detected values for DTN, DON, and Urea-N in the lockdown period decreased by 9.6%, 30.4%, and 28.97%, respectively, compared to 2019. The reduction in human activities is the reason for the decrease. The urban travel intensity in Nanyang city reduced from 6 to 1 during the lockdown period; the 3 million population which should normally travel out from city were in isolation at home before May. The fertilization action to wheat and orange were also delayed.