Chemical pollution in drinking water is of great concern. Organotin compounds (OTCs) are a class of persistent toxic substances with the effect of disrupting endocrine function, but potential human health risk due to organotin pollution in drinking water is still less understood. Understanding the occurrence and sources of OTCs in drinking water is crucial. Seventy drinking water samples collected from tap water, water boiling machines and water vending machines in Shanghai were analyzed for seven target OTCs. It is shown that the summed concentrations of target OTCs (∑OTCs) were up to 129 ng Sn L−1, with the dominant species being dimethyltin (DMT), dibutyltin (DBT), monobutyltin (MBT) and monomethyltin (MMT). Furthermore, OTC pollution levels varied significantly among drinking water types and water source supply zones, with higher ∑OTC concentrations observed in tap water and zone A (supplied by an onshore reservoir next to the estuary). To quantify the sources of OTCs in drinking water, we employed two receptor models for comprehensive comparison: principal component analysis-multiple linear regression (PCA-MLR) and positive matrix factorization (PMF). Both models demonstrated excellent fit to the ∑OTC concentrations, with predicted ∑OTC values from each model showing a significant correlation (r = 0.9822, p < 0.05). Two main sources of OTCs were identified by using both models: materials used in pipes and drinking fountains and emissions from maritime, agricultural and industrial activities, and the PMF model further distinguished sources associated with degradation. The PMF model emerged as the most appropriate model for organotin source apportionment in drinking water due to its detailed and accurate results. In brief, this study revealed that levels of organotin vary across different water sources and supply zones and identified the main sources of pollution from water sources and water supply processes. This research not only addresses critical knowledge gaps but also provides essential information for informing policy and urban planning, particularly regarding the maintenance of community water purification facilities to ensure drinking water quality in rapidly urbanizing regions.