Tejo River Plains, specially “Lezírias” from Vila Franca de Xira, are an important agricultural region where irrigated cultures prevail. Different water sources provide the demand fulfil for the agricultural practices. Surface waters, in particular those from Tejo River, are the most common in the region. Climate change future scenarios would affect hydric availability in quantity or quality. Irrigated cultures are introducing a stress in groundwater bodies where important nitrates concentrations have been already recognized. In addition, irrigation could increase fertilizers leaching to soils and, in depth, groundwater bodies. Ninety-eight water samples with different origins have been analysed and classified according to Piper and Wilcox diagrams. Piper classification was mostly chloride–sulphur–sodium type and Wilcox classification ranged from C1S1 to C4S3 with a great prevalence of C3S1 and C4S2 categories, meaning a salinity hazard that could pose a quality issue and compromising the soil fertility. Groundwater, as being a source where salinity is neglected, could be a valuable option as a water source. Considering it as an option has an increased pressure to groundwater bodies, where regulation and good agricultural practices are solutions to be considered.