Groundwater is one of the crucial water resources for domestic, agriculture and other purposes in the Kurdistan Region of Iraq, which is counted as a semiarid region with seasonal precipitation in winter. The geogenic source of arsenic and fluoride in groundwater has been studied in the Kurdistan Region of Iraq, which is a part of the Zagros Basin, using the hydrogeochemical method. The analysis results showed that the concentrations of arsenic and fluoride range from 0.19 to 7.8 µg/L and from 0.01 to 2.1 mg/L, respectively. The hydrogeochemical characteristics of the groundwater in the studied area were connected to the fluoride F− and arsenic As concentrations for understanding their sources and behavior. The hydrogeochemical relations between F and As indicate geogenic sources and relatively simple aquifer conditions. Some samples may indicate the presence of contamination sources in addition to geogenic sources. Considering the WHO guidelines, the concentrations of As in most of the samples do not exceed the WHO limit, but the F in some samples shows a higher concentration than the WHO limit, indicating a serious risk of fluorosis in some spots. Connecting the changes in F concentrations to depth and aquifer types, a higher F concentration is associated with an intergranular aquifer and decreases in a karst aquifer. The speciation of F− and As is controlled by pH and redox conditions. Adsorption, cation exchange, and the dissolution of carbonate minerals with the possible dissolution of fluorite are the most dominant geochemical processes that control the concentrations of As and F− in groundwater. The principal sources of F− and As in the study area seem to be geogenic.