This study was conducted in order to investigate possible quality changes in Cyprus’ groundwater resources over a 10-year period of pumping and to check the suitability of primary irrigation water. Water samples (n = 890) from private wells in agricultural areas were analyzed from 2009 to 2018 to determine various physicochemical properties. The sodium adsorption ratio (SAR) and residual sodium carbonate (RSC) were also calculated to evaluate potential soil degradation issues. Sodium, chloride and sulphate were found to be the predominant ions in groundwater. Quality evaluation showed possible restrictions in groundwater use for irrigation in relation to its salt content and the toxicity of specific ions having adverse effects on sensitive and several moderately sensitive crops. In particular, an increasing trend was observed in pumped groundwater for boron ion concentrations. Nevertheless, all samples evaluated were suitable for irrigation in terms of soil sodicitation and soil infiltration rate. This study indicates that in order to maintain long-term agricultural sustainability it is imperative to develop strategic plants to mitigate the adverse effects of water-pumped quality deterioration on soils and crops. Precision agriculture techniques may be adapted for better water and nutrient input/output management, thus protecting groundwater from salinization in agricultural areas. These results, among others, may be a useful tool to enhance the ability of Cyprus’s agricultural water sector to adapt to observed and anticipated climate impacts.