Nitrate from farms and villages often seeps into groundwater, threatening water safety. We studied a farming area in northern China across dry, wet, and normal seasons to track and predict nitrate. Nitrate peaked in the dry season due to evaporation, and manure plus household wastewater supplied three quarters of it. Combining artificial data samples with advanced learning methods, we predicted nitrate accurately. This helps officials find pollution hotspots cheaply and protect rural water.