Nitrogen (N) loss from agriculture threatens water quality and affects human health, especially the nitrate leaching. In China, nitrate concentrations in ground-water frequently exceed the World Health Organization (WHO) quality standard for drinking water of 50 mg L−1. In this paper we explore mitigation measures for reducing N loss to water from agriculture. Firstly, we synthesis the current state of nitrate pollution through a review the published literatures. Then, we review measures to mitigate N loss to water. Finally, we present a comprehensive scenario analysis to evaluate the effect of N loss mitigation measures, following a Nitrate Vulnerable Zones (NVZs) approach, similar to that used by EU countries. A combination of balanced N fertilization, precision fertilizer application and irrigation techniques, and a decrease of direct manure discharge into watercourses can decrease N loss from the area of potential designated NVZs by nearly 50% compared to the reference year - 2012. We argue that further research and policy instruments for controlling N loss to water are essential for managing N in crop and livestock production systems in order to protect water quality for human consumption.