Abstarct: Bedrocks and minerals in the groundwater path as well as alterations in rocks are important parameters in the water quality. Water-rock interactions change the concentrations of elements and the quality of water. By increasing the concentration of the elements beyond the standard limits, consumption of water by human and other living organisms cause health problems and environmental impacts. The present research aimed to evaluate the groundwater quality in southern band of Mokhtaran Plain, south of Birjand, as well as assessment of its controlling parameters. Following the collection of available data, field studies, and selection of sampling locations, water samples were collected in two stages, 6 sources in Octobet 2008 (at the end of dry season) and 12 sources in June 2009 (at the end of wet season). Soil and rock samples were also collected from the field. 19 thin sections from the rocks, 13 rock samples for ICP-MS analysis and 18 water samples for measuring cations and anions concentrations and ICP-MS analysis were chosen. According to the environmental priorities and the geological conditions of the region, 12 elements namely: Al, As, B, Ba, Cr, Cu, Fe, K, Pb, Sb, Si, and Zn were selected for further studies. The geological investigations of the area show the presence of volcanic rocks (andesites) and volcanoclastic rocks (tuffs). baxsed on the intensity of alteration in rocks, they were classified in three groups: Group I (weak alteration), Group II (high alteration), and Group III (soils and sediments). Chemical analyses show that in high altered rocks (Group II), Pb, K, and Fe have the highest concentrations while Al, Ba, Cr, Cu, Sb, Zn have the lowest concentrations. Chemical analyses on the water samples and the map of the concentration distribution of the elements, anions and cations, and other parameters show that the alteration causes the increment of the total dissolved solids (TDS), total suspended solids (TSS), and the concentrations of Al, Fe, K, Cu, Pb, Sb, B, Ca, and SO42- and decrement in the concentration of Cr, Ba, and As in water samples. High correlation between the parameters is an evidence of similarity in their geochemical behavior. The highest correlations are calculated between Ca with SO42- (+0.914), Mg with Si (+0.800), B with TDS (+0.973), B with Cl (+0.967) and B with Na (+0.994) in water and Ca with Sr (+0.884) and Fe with K (+0.901) in rocks. Calculation of mextal index (MI) for water resources indicates that Bidokht Spring and Roode Kaj, Yoush, and Bidestan qanats, as well as Kooshe, Valiasr, and Doulatabad wells have MI bigger than 1. Montmorilonite, Kaolinite, Hematite, Goethite, and iron hydroxides are among the minerals in water resources with the saturation index (SI) bigger than zero and thus with high probability of sedimentation. Alteration has caused the augmentation in variation of SI for some minerals in water resources. In accordance with geological, petrological, and geochemical studies, element distribution map in water resources, correlation table of elements in water and rock, and SI diagram, a conceptual model was developed to interpret the water-rock interaction and transportation and transformation of the elements from intermediate media into the water. In this model, elements from the primary media including primary rocks, altered rocks by hydrothermal fluids, and possible mineralization enters into the intermediate media through weathering, and other chemical reactions. Finally, by washing and reactions such as solution, ion exchange, and desorption these elements appear in water resources. In the case of saturation in the solution by the elements and ions, sedimentation occurs and elements are extracted from the liquid phase.