In this study, the crop yield response of rainfed crops to climate change was evaluated focusing on the most representative crops in the Guadiana river basin. The quantification of crop yields was performed using a simple soil water balance model framework. The herbaceous crop yields were evaluated with the ISAREG model, implementing a water balance approach combined with the Stewart method. A similar water balance approach was used to estimate the yields for the most representative permanent rainfed woody crops in the region using an alternative spreadsheet-based model, but implementing a more detailed water stress evaluation through the crop cycles. Yields were simulated for two future periods (2011–2040) and (2041–2070) using, as climate inputs, temperature and precipitation series, reflecting a combination of five climate change scenarios (CCS) created using the ensemble-delta technique applied to CMIP3 climate projections datasets to represent different alternative climate change bracketing conditions for rainfall and air temperature. The results showed that comparatively with the reference period climate (1961–1990) rainfed crop yields will decrease in future period 1 (2011–2040) and reach even higher losses in future period 2 (2041–2070). Within the herbaceous crops, sunflower and winter wheat were the most susceptible to yield losses under climate change, reaching estimated maximum losses for future period 2 of respectively 18.5% and 13.6%, followed by natural grown pastures with 11.5%. For woody crops, maximum estimated yields losses were considerably higher for almond (27.2%) than grapevine (5.4%) and olive (14.9%).