In the Po plain, northern Italy, rivers within agricultural basins display steep summer increases in nitrate (NO3−) concentrations. Flood irrigation in overfertilized, permeable soils may drive such diffuse pollution, facilitating interactions between NO3−-rich groundwater and surface waters. We discuss multiple, indirect evidence of this mechanism in the Adda, Oglio, and Mincio rivers. These rivers drain agricultural soils with elevated nitrogen (N) surpluses, averaging 139, 193, and 136 kg ha−1 in the Adda, Oglio, and Mincio watersheds, respectively. The three rivers cross a transitional area between highly permeable and impermeable soils, where summer NO3− concentrations may increase by one order of magnitude over short distances (8–20 km). Upstream of this transitional area, a major fraction of the river flow is diverted for flood irrigation, a traditional and widespread irrigation technique for permeable soils. We speculate that diverted water solubilizes soil N excess, recharges the aquifer, and transfers soil N surplus into groundwater, resulting in NO3− pollution. Groundwater–river interactions were estimated experimentally, via water and NO3− budgets in 0.3 to 1 m3 s−1 km−1 and in 1500 to 5400 kg NO3−–N day−1. The data suggest a pronounced east–west gradient of groundwater to river diffuse water inputs among the three adjacent basins, reflecting the soil permeability and the width of the river–groundwater interaction zone. Given the large stock of NO3− in groundwater, management interventions performed at the basin scale and aimed at decreasing N excess will not produce an immediate decrease in river NO3− pollution.