The protozoa Cryptosporidium and Giardia are major causes of diarrhea and are commonly found on vegetables in China. They pose a health risk, particularly to immunocompromised individuals, including cancer patients. A quantitative microbial risk assessment of Chinese data evaluated the risks of Cryptosporidium and Giardia exposure arising from the application of surface water and septic tank effluent to agricultural land. Exposure via agricultural produce consumption (consumers) and agricultural practices (farmers) was considered for subpopulations of cancer patients and immunocompetent people in urban and rural areas, and risk mitigation scenarios were modelled. The cumulative disease burdens attributable to cryptosporidiosis and giardiasis were, respectively, 9.68×10−6 and 5.57×10−5 disability-adjusted life years per person per year (DALYs pppy) for immunocompetent people, and 3.14×10−5 and 1.51×10−4 DALYs pppy for cancer patients. Cancer patients were approximately three times more likely to have an individual disease burden than immunocompetent people. The disease burden was higher for consumers than farmers, and higher in rural areas than urban areas (all exceeding the maximum recommended by the World Health Organization). The highest burdens were in provinces of high population, such as Henan, Guangdong, and Sichuan, while the burden associated with human and livestock fecal effluent application was higher than with surface water irrigation. Of the three vegetables studied, lettuce posed the greatest risk, followed by bok choy, while cucumber posed the least risk. Risk mitigation scenario analysis showed that pre-treatment of surface water and feces, and appropriate post-harvest handling of vegetables, including disinfection, cooking, and adequate surface heat treatment (75 °C for 60 s), should be considered when attempting to reduce disease burdens. The methodology and findings of this study are useful for evaluating and reducing the burden of Cryptosporidium and Giardia infections associated with agricultural irrigation and fertilization practices, particularly on cancer patients.