In the context of the management of bathing water quality, the intermittent contamination of rainwater drainage pumps (unconventional point sources) could be controlled by peracetic acid disinfection. Thus, a field experimental study was carried out to set up a water safety plan, determining the monitoring parameters and the critical limit for corrective actions. With a 0.5 mg/l dosage, the average logarithmic microbial reduction was 0.50 ± 0.48 for Escherichia coli (EC) and 0.43 ± 0.54 for intestinal enterococci. Among the chemical and physical parameters that could be monitored in real time, the oxidation–reduction potential was the only one able to predict the microbial concentration discharged from a drainage pump and the logarithmic abatement of EC. Considering the possible impact of this source on bathing waters in terms of additional risk of gastrointestinal infections, the critical limit for continuous monitoring was established using a quantitative microbial risk assessment (QMRA) model.