Rainwater is considered a dependable source for domestic purposes within rural areas in Palestine. Harvested rainwater stored in cisterns is used to leverage deficits from municipal water supplies. Harvested rainwater in areas surrounded with industrial and agricultural activities is usually contaminated with heavy and trace metals. To study the effects of human exposure to heavy and trace metals, 74 harvested rainwater samples of rain-fed cisterns were collected from different localities in the Yatta area of Palestine in the months of January and February of 2016. The water samples were analysed for Ca, Mg, Al, Fe, K, Na, Ag, Li, Co, Ba, Bi, Sr, Ga, V, Rb, Mo, Beand Tl elements utilizing ICP-MS (inductively coupled plasma mass spectrometry). The selected trace metals were found within the concentration limits of the acceptable values, in accordance with WHO and Palestinian standards, except for K and Al, which were found above the allowed limits. The potential risks of the selected trace metals on the health of the local residents, as well as the possible sources of such heavy metals, were also studied. The Chronic daily intake (CDI) of each metal and health risk indexes (HRI) were calculated for both adults and children residents. The oral ingestion pathway was studied, including exposure via drinking water. The values for CDI were found in the descending order of: Ca > Mg > Na > K > Sr > Fe > Al > Ba > Li > V > Rb > Ag > Mo > Ga > Co > Bi > TI > Be. The values of HRI were below 1 for most of the selected heavy metals, expect for Li for children, indicating potential health risk. The study also predicted that the local residents have a higher chance of developing cancer in their lifetime, especially children, with respect to the carcinogenic risk (CRing) values for Na, Mg, Al, Ba, K, Ca, Fe and Sr, which were greater than standardized limits (>10−6). The rest of the selected elements were within the acceptable limit in the five different studied locations. Furthermore, univariate, multivariate and statistical analysis depending on one-way ANOVA, inter-metal correlation, cluster analysis (CA) and principal component analysis (PCA) results revealed that geogenic and anthropogenic activities were major sources of drinking water contamination by heavy metals in the Yatta area.