A quantitative microbial risk assessment (QMRA) was conducted to support renewal of the City of Vacaville wastewater discharge permit and seasonal (summer) filtration requirements. Influent and final disinfected effluent from the city's wastewater treatment plant, as well as 11 receiving water stations, were monitored for indicator organisms (i.e. total and fecal coliforms, Escherichia coli, Enterococcus, male-specific bacteriophage (MS2), and the Bacteroidales) and several pathogens (i.e. Giardia cysts, Cryptosporidium oocysts, infectious Cryptosporidium, and Norovirus GI and GII). QMRA annualized risks of infection for selected pathogens enteric viruses, Giardia and Cryptosporidium. Estimated median annualized risk for recreational exposure in either disinfected secondary and/or filtered disinfected secondary effluent is on the order of 1.1 × 10−3 per person per year (pppy) for enteric viruses and would be roughly one order of magnitude lower if local receiving water dilution of the treatment plant effluent was taken into account. Estimated median annual risk for recreation exposure in disinfected secondary effluent is 1.8 × 10−3 pppy for Cryptosporidium and 1 log10 less with filtration during the summer months. The estimated median annual risk for landscape exposure (e.g. golfing) to secondary disinfected effluent is 7.6 × 10−7 pppy for enteric viruses. Estimated median annualized risk is 1.7 × 10−7 pppy for enteric viruses and 3.0 × 10−5 to 3.6 × 10−6 pppy for parasites for use of secondary disinfected effluent with irrigated agriculture. Estimated annualized risks for recreational exposure to the local receiving waters were approximately 10 to 1,000 times greater than direct recreational exposure to the final filtered and disinfected effluent. All risk estimates associated with exposure to final treated plant effluent (i.e. secondary filtered and disinfected) were close to or lower than the California level of acceptable annual risk of infection of 10−4 pppy for recreational exposure. Risk estimates provide further evidence to support the use of seasonal treatment limits requiring summer filtration for public health protection.