A steady increase in bacteria loading has been found along the Lower Neches River and in coastal waters in recent years. The source of increase has not been well understood, but a possible contributor is increasing incidence of failures of aged on-site sewage facilities (OSSFs) tied to more frequent occurrence of extreme flooding in recent years. As increasing bacteria presence prompts water quality and health concerns in Southeast Texas Gulf coastal communities, there is an urgent need to determine the origin and transport pathways of the bacteria, and identify and assess countermeasures. Historic water quality data analysis demonstrates that the flow rate is positively correlated with E-coli, TSS, and turbidity. The correlation between E-coli and turbidity suggests that turbidity > 45 NTU in the Lower Neches River can serve as an indicator of bacterial outbreak, as such turbidity often occurs after the first flush of heavy rain events. The project team conducted a field survey over locations downstream of OSSFs and identify a total of 14 sites in the drainage system to collect water samples based on the field geology, hydraulics, and age of OSSFs. Field and lab measurements of two sets of water samples after rain events illustrates the elevated E. coli were detected in the area with increasingly aged OSSFs. The ongoing efforts focus on further analysis of the field water samples, establishment of an SWMM-based modeling system for understanding the bacteria transport pathways and assessing BMPs to alleviate the excess loadings.