Self-supplied wells, an important water resource in remote and scattered regions, are commonly deteriorated by environmental pollution and human activity. In this study, 156 self-supplied well-water samples were collected from remote and scattered areas of Inner Mongolia (NMG), Heilongjiang (HLJ), and the suburbs of Beijing (BJ) in Northern China. Twenty-four heavy metals were identified by using the inductively coupled plasma-mass spectrometry (ICP-MS) and inductively coupled plasma-optical emission spectrometry (ICP-OES), and the associated human health risks were assessed by using standards of the US Environmental Protection Agency (US EPA). The concentrations of four heavy metals (As, Fe, Mn, and Tl) in HLJ, one heavy metal (Tl) in BJ, and ten heavy metals (Al, As, B, Cr, Fe, Mn, Mo, Se, Tl, and Zn) in NMG exceeded the limits set by China or the World Health Organization (WHO). The total carcinogenic risk (TCR) and total non-carcinogenic risk (THQ) exceeding set limits mainly occurred in NMG, compared to HLJ and BJ. Moreover, As accounted for 97.87% and 60.06% of the TCR in HLJ and BJ, respectively, while Cr accounted for 70.83% of the TCR in NMG. The TCR caused by Cd in all three areas had a negligible hazard (<10−4). As accounted for 51.11%, 32.96%, and 40.88% of the THQ in HLJ, BJ, and NMG, respectively. According to the results of the principal component analysis, heavy metals in well water from HLJ and NMG mainly originated from mixed natural processes and anthropogenic sources, whereas, in BJ, most heavy metals probably originated from natural sources. In the future, long-term monitoring of heavy metals in water from self-supplied wells should be conducted for an extensive range of well-water sites, and well water with high As contamination should be monitored more and fully assessed before being used as a drinking-water source.