Owing to increasing anthropogenic impacts, wetlands have suffered a serious environmental decline in recent decades. The sustainable management of these natural resources is fundamental to maintain both the ecosystems and the economic activities. The Lake Massaciuccoli and nearby areas represent one of the largest residual coastal marshy areas in Tuscany (Italy). This wetland is characterized by large-scale and intensive agricultural use and affected by reclamation activities, with consequent problems of erosion, subsidence and lake eutrophication and siltation. In this context, an integrated study combining hydrochemical data (water levels, electrical conductivity, pH, turbidity, major ions, trace metals) and stable isotopes (H, O, S) has been performed in the southernmost part of the basin, to better disentangle processes and interactions between groundwater and surface water and to understand the origin of solutes and their evolution. Our results indicated that both groundwater and surface water have a meteoric origin and that geochemical composition of groundwater is mainly affected by local geological and biological processes. Moreover, surface water is affected by sea water mixing and evapotranspiration/precipitation processes. The impact of agricultural activity and the use of fertilizers on the water quality appears to be limited as regards nitrates, indicating that less intense agricultural practices implemented in recent years have been successful. As regards sulfates, Fe, and Mn, we cannot fully elucidate the mechanisms underlying human influence, but the oscillation of water level and degradation of peat enhanced by reclamation and agriculture activities likely played an important role in controlling the fate of these elements. Overall, these results underline the importance of integrated approaches to disentangle geochemical processes and will be useful in supporting policy implementation and environmental protection in this valuable area of Tuscany. Findings from this work suggest the need for policy-making authorities to take actions as soon as possible to mitigate risks. Closer co-operation is essential between authorities and farmers to reduce inputs of fertilizers and chemicals into the lake and the surrounding area. Also, additional policy measures should be enforced to reduce the mechanical soil tillage and limit erosion and runoff, such as the NBSs implemented within the Phusicos Project.