Pond irrigation water comprises a major pathway of pathogenic bacteria to fresh produce. Current regulatory methods have been shown to be ineffective assessing this risk when variability of bacterial concentrations is large. This paper proposes using mechanistic modeling of bacterial transport as a way to identify improved strategies for mitigating this risk pathway. If the mechanistic model is successfully tested against observed data, global sensitivity analysis (GSA) can identify important mechanisms to inform alternative, preventive bacterial control practices. Model development favored parsimony and prediction of peak bacterial concentration events. Data from two highly variable surface water irrigation ponds showed that the model performance was similar or superior to existing pathogen transport models, with a Nash-Sutcliffe efficiency of 0.48 and 0.18 for the two ponds. GSA quantified bacterial sourcing and hydrology as the most important processes driving pond bacterial contamination events. Model analysis has two main implications for improved regulatory methods: that peak concentration events are associated with runoff-producing rainfall events; and that intercepting bacterial runoff transport may be the best option to prevent bacterial contamination of surface water irrigation ponds, and thus, fresh produce. This research suggests the need for temporal management strategies. Importance Preventive management of agricultural waters requires understanding of the drivers of bacterial contamination events. We propose mechanistic modeling as a way forward to understand and predict such events and have developed and tested a parsimonious model for rain-driven surface runoff contributing to generic Escherichia coli contamination of irrigation ponds in Central Florida. While the model was able to predict the timing of peak events reasonably well, the highly variable magnitude of the peaks was less well predicted. This indicates the need to collect more data on the fecal contamination inputs of these ponds and the use of mechanistic modeling and global sensitivity analysis to identify the most important data needs.