Saline wetlands are highly sensitive to anthropogenic pressures, particularly in semi-arid regions where groundwater abstraction, land use changes, and climate variability modify their hydrogeological functioning. This study focuses on the Tirez and Penahueca hypersaline wetlands (Central Spain), which have undergone a shift from natural groundwater discharge zones to induced recharge areas due to intensive irrigation. Declining piezometric levels have reversed the hydraulic gradient between the aquifer and the wetlands, resulting in recharge conditions. A multidisciplinary approach combining hydrochemistry, (including historical monitoring data), multi-isotopic characterization (N, O, C, S), and geophysical (ERT) techniques was applied to assess groundwater quality evolution and nitrate attenuation processes. Results show a significant increase in groundwater salinity and nitrate concentrations over the past five decades, with NO3- levels reaching up to 245 mg/L. Average nitrate concentrations increased from similar to 25 mg/L in the 1990s to over 200 mg/L in 2019-2021. Isotopic signatures indicate multiple nitrate sources, including manure, organic soil nitrogen, and synthetic fertilizers. A coupled increase of delta N-15-NO3- values ranging from +5.1 parts per thousand to +44 parts per thousand and delta O-18-NO3- from +3 parts per thousand to +23 parts per thousand, along with delta S-34-SO42- values between +16 parts per thousand and + 18 parts per thousand and delta C-13-DIC from -12 parts per thousand to -4 parts per thousand, suggest that heterotrophic denitrification is the main attenuation process. Electrical resistivity profiles reveal density-driven flow from the saline wetland water into the underlying aquifer, facilitating the transport of dissolved organic carbon and creating redox gradients favorable for denitrification. Maximum denitrification rates of up to 73% were estimated using literature isotopic fractionation values. Understanding the coupled hydrological and biogeochemical dynamics of saline wetland-aquifer systems is essential for developing sustainable groundwater management strategies in vulnerable arid and semi-arid regions.