The variability of fecal microorganisms and wastewater micropollutants (WWMPs) loads in relation to influent flow rates was evaluated for a water resource recovery facility (WRRF) in support of a vulnerability assessment of a drinking water source. Incomplete treatment and bypass discharges often occur following intense precipitation events that represent conditions that deviate from normal operation. Parasites, fecal indicator bacteria, and WWMPs concentrations and flow rate were measured at the WRRF influent and effluent during dry and wet weather periods. Influent concentrations were measured to characterize potential bypass concentrations that occur during wet weather. Maximum influent Giardia and C. perfringens loads and maximum effluent Escherichia coli and C. perfringens loads were observed during wet weather. Influent median loads of Cryptosporidium and Giardia were 6.8 log oocysts/day and 7.9 log cysts/day per 1,000 people. Effluent median loads were 3.9 log oocysts/day and 6.3 log cysts/day per 1,000 people. High loads of microbial contaminants can occur during WRRF bypasses following wet weather and increase with increasing flow rates; thus, short-term infrequent events such as bypasses should be considered in vulnerability assessments of drinking water sources in addition to the increased effluent loads during normal operation following wet weather.