Soil salinity is a major soil degradation threat especially for arid coastal environments where it hinders agricultural production, thus imposing a desertification risk. In the prospect of a changing climate, soil salinity caused by brackish water irrigation introduces additional uncertainties regarding the viability of deficit irrigation and intensive cultivation practices such as greenhouse cropping. Here, we propose a modification of the SALTMED leaching requirement model to account for greenhouse cultivation conditions. The model is applied in the RECARE Project Case Study of Timpaki, a semiarid region in south-central Crete, Greece, where greenhouse horticulture is an important land use. Excessive groundwater abstractions toward irrigation have resulted in a drop of the groundwater level in the coastal part of the aquifer, thus leading to seawater intrusion and in turn to soil salinization. Crop yield and soil profile electrical conductivity (EC) sensitivity to initial soil EC (up to 2 dS m−1) and irrigation water EC (up to 3 dS m−1) are modeled for the locally popular horticultural crops of Solanum lycopersicum, Solanum melongena, and Capsicum annuum. Climate model data obtained from nine general circulation models for the “worst case” representative concentration pathway of 8.5 W m−2 of the fifth phase of the Coupled Model Intercomparison Project are corrected for bias against historical observations with the Multisegment Statistical Bias Correction method and used to estimate crop yield and soil profile EC sensitivity in a warmer future. Results show that the effects of climate change on S. lycopersicum greenhouse cultivations of Timpaki will be detrimental, whereas S. melongena and C. annuum cultivations may show greater resilience.