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The conversion of cultivated areas from rainfed to irrigated agriculture alters the watershed’s hydrology and could affect the water quality and quantity. This study examined how streamflow, nitrate load, and nitrate concentration changed after irrigation implementation in a Mediterranean watershed in Navarre, Spain. The Soil Water Assessment Tool (SWAT) model was applied in the Cidacos River watershed to simulate streamflow and nitrate load under rainfed conditions. The simulated outputs were then compared with the post-irrigation observed values from mid-2017 to 2020 at the watershed outlet in Traibuenas to determine the irrigation impact. The model calibration (2000–2010) and validation (2011–2020) results for streamflow (NSE = 0.82/0.83) and nitrate load (NSE = 0.71/0.68) were satisfactory, indicating the model’s suitability for use in the watershed. A comparison of the rainfed and post-irrigation periods showed an average annual increase in streamflow (952.33 m3 ha−1, +18.8%), nitrate load (68.17 kg ha−1, +62.3%), and nitrate concentration (0.89 mg L−1 ha−1, +79%) at the watershed outlet. Irrigation also caused seasonal changes by altering the cropping cycle and increasing the streamflow and nitrate export during the summer and autumn when irrigation was at its peak. The increases in the post-irrigation period were attributed to the added irrigation water for streamflow and increased nitrogen fertilizer application due to changes in cropping for nitrate concentration and export. These findings are useful to farmers and managers in deciding the best nitrate pollution control and management measures to implement. Furthermore, these results could guide future development and expansion of irrigated lands to improve agricultural sustainability.