The main objective of this paper is to analyze the impact of climate change on water resources management and groundwater quantity and quality in the coastal agricultural Almyros Basin, in Greece. Intensive groundwater abstractions for irrigation and nitrogen fertilization for crop production maximization, have caused a large water deficit, nitrate pollution, as well as seawater intrusion in the Almyros aquifer system. Multi-model climate projections for Representative Concentration Pathways (RCPs 4.5 and 8.5) from the Med-CORDEX database for precipitation and temperature have been used to evaluate the impacts of climate change on the study area. The multi-model climate projections have been bias-corrected with Delta, Delta change of Mean and Variance, Quantile Delta Change, Quantile Empirical Mapping, and Quantile Gamma Mapping methods, and statistically tested to find the best GCM/RCM multi-model ensemble. Simulation of coastal water resources has been performed using an Integrated Modelling System (IMS) that contains connected models of surface hydrology (UTHBAL), groundwater hydrology (MODFLOW), nitrate leaching/crop growth (REPIC), nitrate pollution (MT3DMS), and seawater intrusion (SEAWAT). The results indicate that the best climate multi-model ensemble consists of three (3) climate models for both RCP4.5 and RCP8.5 using the Quantile Empirical Mapping bias-correction method. The IMS was applied for historical and future periods with observed and simulated meteorological inputs (e.g. precipitation and temperature) and various irrigation and agronomic scenarios and water storage works development (i.e. reservoirs). The results indicate that at least deficit irrigation and deficit irrigation along with rain-fed cultivation schemes, combined with or without the development and operation of reservoirs, should be applied to overcome the degradation of groundwater quality and quantity in the study basin. Based on the findings of this work, the water resources management should be adaptive to tackle the water resources problems of the Almyros Basin.