Environmental isotopes data of oxygen and hydrogen of natural water and sulphur and oxygen of dissolved sulphate as well as characteristics of d-excess are used to illustrate the salinity origin in Kert aquifer NE Morocco. In this study, 14 groundwater samples and surface water of the Kert River were collected in the Kert plain during December 2008, and were combined with previously collected hydrochemical data. The isotope compositions of these waters range from −5.74 to −4.51 ‰ for oxygen and from −40.8 to −34.1 ‰ for hydrogen. In Kert River these values are −6.47 ‰ for oxygen and −47.56 ‰ for hydrogen. All the samples with a slope <8 do not fall on the meteoric water line indicating a light evaporation. Water has low and different d-excess values (ranging from +1.37 to +9.82 ‰), reflecting different climatic conditions. Based on the nitrate concentration water in the Kert aquifer comes from the modern precipitation. The isotope compositions range from −2.2 to +16 ‰ for sulphur and from +5.02 to +13.86 ‰ for oxygen. In Kert River these values are −4.6 and +5.3 ‰ for sulphur and oxygen, respectively. There are fairly constant difference between oxygen of water and the oxygen of sulphate suggesting a dominant control of this latter in sulphate sources. At least three major sulphate sources were identified by the isotope data from sulphate in these waters: (1) dissolved marine sulphate from the underlying upper Miocene unit; (2) dissolved sulphate from Kert River; (3) sulphate derived from oxidation of sulphur compounds in the metamorphic massif of Temsamane. The latter has a dilution role. The isotopic variations of these waters and sulphate concentration therein reflect mixing of these sources in the aquifer.