The conventional point-estimate human health risk assessment (HHRA) primarily uses average concentrations of a limited number of samples due to the high monitoring costs of heavy metals in groundwater. The results can be erroneous when concentrations significantly deviate from the average across the collected samples in an investigation region. The present research developed a hierarchical fuzzy-based HHRA (F-HHRA) framework to handle variations in limited data sets and subjectively established a broader range of risks for various exposure groups. Groundwater samples from 80 to 120 m deep in shallow wells were collected from agricultural farms along Wadi Rumah in the Qassim Region of Saudi Arabia. Laboratory testing found total dissolved solids much higher than the promulgated drinking water quality standards. As the aftertaste issue eliminated the raw water potability, the study considered dermal exposure for HHRA. The collected samples were tested for thirteen potential heavy metals (HMs), including barium (Ba), boron (B), cadmium (Cd), chromium (Cr), copper (Cu), iron (Fe), lead (Pb), lithium (Li), manganese (Mn), silver (Ag), strontium (Sr), thallium (TI), and zinc (Zn). Cu, Fe, Pb, Ag, and TI were lower than the detectable limit of the inductively coupled plasma mass spectrometry device. Concentrations of the remaining HMs in wastewater outfalls that were much less than the groundwater eradicated the impact of anthropogenic activities and affirmed natural contamination. Apart from 10% of the samples for Mn and 90% of the samples for Sr, all the other HMs remained within the desired maximum allowable concentrations. Point-estimate and fuzzy-based approaches yielded ‘low’ dermal non-cancer risk and cancer risk for all groups other than adults, where dermal cancer risk of Cr remained in the ‘acceptable’ (1 × 10−6 and 1 × 10−5) risk zone. Although dermal risk does not require controls, scenario analysis established the rationality of F-HHRA for more contaminated samples. The proposed hierarchical F-HHRA framework will facilitate the decision-makers in concerned agencies to plan risk mitigation strategies (household level and decentralized systems) for shallow well consumers in Saudi Arabia and other arid regions.