In the last decades, the intensification of agricultural practices has deeply altered nitrogen (N) and water cycles. Climate change and drought events are expected to further increase the human impacts on the hydrological and biogeochemical cycles, and these impacts are gaining the attention of the scientific community. Here we show how the Chiese River watershed (Lombardy Region, Italy) represents an interesting opportunity to analyse the effects of traditional irrigation practices on N contamination in the context of water scarcity. During summer, flood irrigation is mostly sustained by groundwater withdrawal. Additional water withdrawals from the river contribute to the dry out of the Chiese River. The use of wells for irrigation over permeable and fertilized soils and the percolation of nitrate (NO3-) from the vadose zone to groundwater result in the accumulation of NO3- in groundwater and limited N losses via denitrification due to dominant oxic conditions. These practices contrast other measures targeting the reduction of N excess over arable land. In the Chiese River watershed, the N surplus from Soil System Budget calculations decreased by 43% since the early 2000 s but NO3- concentration in groundwater remained high and stable (up to 98.0 mg NO3- L−1). The dried-out Chiese River gains groundwater and NO3- concentration at the river mouth approaches 32.2 mg NO3- L−1. Our results suggest how the mismanagement of the watershed (overabundant fertilization and flood irrigation using groundwater) increases the N concentration both in the river and groundwater, leading to the violation of both Nitrate and Water Framework directives. We anticipate our assay to be a starting point for the conversion of the northern Po Plain to more efficient irrigation and fertilization practices to contrast severe droughts driven by climate change like the one who struck the Po Plain in summer 2022.