Nitrate is globally the most widespread and widely studied groundwater contaminant. However, few studies have been conducted in sub-Saharan Africa, where the leaching potential is enhanced during the rainy monsoon phase. The few monitoring studies found concentrations over drinking water standards of 10 mg N-NO3− L−1 in the groundwater, the primary water supply in rural communities. Studies on nitrate movement are limited to the volcanic Ethiopian highlands. Therefore, this study aimed to evaluate the transport and fate of nitrate in groundwater and identify processes that control the concentrations. Water table height, nitrate, chloride, ammonium, reduced iron, and three other groundwater constituents were determined monthly in the groundwater in over 30 wells in two contrasting volcanic watersheds over two years in the Ethiopian highlands. The first watershed was Dangishta, with lava intrusion dikes that blocked the subsurface flow in the valley bottom. The water table remained within 3 m of the surface. The second watershed without volcanic barriers was Robit Bata. The water table dropped rapidly within three months of the end of the rain phase and disappeared except near faults. The average nitrate concentration in both watersheds was between 4 and 5 mg N-NO3− L−1. Hydrogeology influenced the transport and fate of nitrogen. In Dangishta, water was blocked by volcanic lava intrusion dikes, and residence time in the aquifer was larger than in Robit Bata. Consequently, nitrate remained high (in several wells, 10 mg N-NO3− L−1) and decreased slowly due to denitrification. In Robit Bata, the water residence time was lower, and peak concentrations were only observed in the month after fertilizer application; otherwise, it was near an average of 4 mg N-NO3− L−1. Nitrate concentrations were predicted using a multiple linear regression model. Hydrology explained the nitrate concentrations in Robit Bata. In Dangishta, biogeochemistry was also significant.