Lowland coastal areas as the Po Delta (Italy) are often intensively cultivated and affected by nitrogen imbalance due to fertilizers leaching to groundwater and export via run-off. To address this issue several agricultural best practices have been proposed, like limiting the amount of fertilizers and increasing soil organic matter content. In this study, groundwater samples were analysed for major ions and stable isotopes of HO, C, N and S using multi-level sampler (MLS) from two contrasting depositional environments, one representative of alluvial plain (AP) and the other representative of a reclaimed coastal plain (RCP). In each site, controlled plots with different agriculture practice including fertilizers and tillage and compost amendment and no tillage were considered in the study. Tracer test results highlight that recharge water infiltrated at the start of the controlled study has not yet reached the saturated zone, thus current groundwater concentrations are representative of former agricultural practices. Stable isotopes show a clear distinction between different sources of nitrogen in both sites, from synthetic fertilizers to sedimentary nitrogen pool and atmospheric input. The main source of sulphate in groundwater is pyrite and fertilizers. Denitrification, sulphate reduction and methanogenesis were involved in the C, N and S cycle in the RCP site characterized by low hydraulic conductivity sediments and high SOM. These processes were not relevant in the AP site characterized by oxic condition and low SOM, but some evidence of denitrification was found in one of the AP sites. High resolution monitoring was a key tool to identify the different redox zones responsible for N, C and S cycling in these aquifers. This study shows that a clear understanding of transit times in the vadose zone is a key prerequisite to evaluate the effect of controlled agriculture practice on the quality of shallow groundwater.