Accessibility to quality drinking water is essential for public health. The World Health Organization (WHO) states that drinking water quality must be regularly evaluated to ensure it meets microbiological, chemical, and physical safety criteria. The objective of this study was to determine the quality of drinking water at the point of use in Indonesian households, with a focus on the effectiveness of boiling as a water treatment method. A cross-sectional study was conducted using data from 25,000 randomly selected households across 514 districts and cities in Indonesia. Drinking water samples were collected from household storage containers and tested for Total Dissolved Solids (TDS), pH, Escherichia coli (E. coli), total coliforms, nitrates, nitrites, and hexavalent chromium (Cr⁶⁺) using standardized field testing kits. Of the households surveyed, 37.6% consumed bottled or refilled water, 55.5% used water from protected sources, and 6.9% relied on unprotected sources. Boiling was significantly associated with improved drinking water quality, particularly in terms of reductions in total coliforms, Cr⁶⁺, pH, and TDS levels (p < 0.05). The strongest associations were observed for TDS (OR = 1.44, 95% CI: 1.30–1.60) and pH (OR = 1.43, 95% CI: 1.34–1.53). Boiling water effectively treats water quality, but it must be appropriately stored to prevent contamination. Public health interventions should promote water treatment and safe storage to reduce the risk of waterborne diseases in Indonesian households.