In the Guadalhorce river basin (South Spain) diverse water resources come together: rivers, aquifers and reservoirs. Sampling campaigns carried out in previous years show that both the chemical quality and the isotopic signal of water supply and irrigation water vary according to different factors of anthropogenic (existence of reservoirs with different water quality, irrigation channels and groundwater pumping) and natural origin (precipitation variability between dry, medium and wet years). This situation modifies the waters isotopic signal between surface and groundwater in different zones of the basin (upper and lower basin) and its mineralization. There is an isotopic enrichment in the water molecule (δ18O, δ2H) and an increase in chloride concentration along the groundwater flow. Water isotope signatures reveal that the majority of groundwater samples seem to be affected by evaporation processes (samples in a δ18O-δ2H graph are plotted over an evaporation line of slope 4-5). In a δ18O/Cl- plot it is also detected an isotopic enrichment in the water molecule but in combination with chloride concentration along the flow line. The relationship between δ18O/Cl- at the upper and lower part of the basin is different with the quantity of rainfall. While at the upper part there are no changes in chloride concentration or isotopic enrichment between wet, medium or dry years at the lower part, we find variations over dry or medium rainfall years, which are those that occurred in the study campaigns. It’s considered that a variety of processes coexist: the influence of the water stored in the reservoirs; the isotopic fractionation of water during pumping and irrigation return processes; and mixing processes with surface water of better quality.