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Cryptosporidium and Giardia (major causes of diarrhea) are widely distributed in Chinese source waters and threaten human health. A new spatially explicit GloWPa-TGR-Crypt-Giar C1 model is presented to simultaneously estimate mean monthly (oo)cyst concentrations in surface and ground waters in the Three Gorges Reservoir (TGR) watershed. A quantitative risk assessment of protozoal infections considered different source waters, transmission pathways, regions, susceptible subpopulations, and drinking water treatments. Monthly mean Cryptosporidium oocyst and Giardia cyst concentrations ranged between 0.5–19.3 oocysts/10 L and 0.2–5.0 cysts/10 L in surface water, respectively, and 0.007–0.3 oocysts/10 L and 0.002–0. 2 cysts/10 L in groundwater. The cumulative disease burdens attributable to cryptosporidiosis and giardiasis were, respectively, 5.77×10−5 DALYs (disability-adjusted life years/person/year) and 4.63×10−6 DALYs in urban areas, and 6.35×10−4 DALYs and 8.84×10−5 DALYs in rural areas, which were much higher than the reference risk level recommended by the World Health Organization ($${10}^{-6}$$ 10 - 6 DALYs). The annual burden associated with consuming surface water was calculated to be 3.84×10−4 DALYs for Cryptosporidium and $$5.10\times {10}^{-5}$$ 5.10 × 10 - 5 DALYs for Giardia, whereas consuming groundwater entailed the lower burdens (1.26×10−5 and 3.50×10−6 DALYs, respectively). Most DALYs were a consequence of consumption of directly supplied surface water. Fifty percent of the health burden was carried by immunodeficiency with HIV. Children (0–4 years) were more likely to have an individual disease burden than adults (15–64 years). Males were more susceptible than females. Improving sanitation through adequate ozone and microfiltration treatment should be considered when attempting to reduce disease burden. Sensitivity analysis highlighted the importance of reducing (oo)cyst loads to protect the watershed. The methodology and results described will help in evaluating and reducing the burden of protozoal infection associated with surface and ground waters in the TGR and similar watersheds. Graphical Abstract