Protecting human health from recreational waterborne illness is at the heart of every microbiological monitoring program of recreational waters in the world. Also, monitoring of recreational beaches helps to keep these aquatic environments healthy. However, measuring fecal indicator bacteria (FIB) at these sites can negatively affect local economies due to beach and shellfishery closures and expensive source tracking studies aimed at lowering FIB concentrations in the effected water bodies. This dissertation investigates the sources, fate, transport, and ecology of FIB in two different settings located in southern California: (1) at a freshwater recreational site that is influenced by both highly treated wastewater effluent and urban runoff, and (2) at a marine recreational beach impacted with raw sewage from old leaking sewer lines.

The Middle Santa Ana River, located in Riverside California, is a large river dominated by wastewater effluent. This site was investigated for sources of microbial contamination from either treated wastewater effluents and/or urban runoff using traditional culture-dependent assays of FIB, culture-independent assays, and chemical fecal markers, and recommends moving from the “one-size-fits-all” FIB criteria currently in place by the Environmental Protection Agency toward site-specific criteria. Furthermore at this field site, the flux of FIB from within the sediment bed into the overlying water column was found to be controlled by physical processes operative at the sediment-water interface.

The marine recreational beach is located in the City of Avalon on Santa Catalina Island. Here we determined two stretches of beach most likely to have FIB contaminated shallow groundwater and pore fluids using a combination of monitoring-well and beach trench studies. We determined that transport of contaminated shallow groundwater into nearshore waters is most likely from tidally driven submarine groundwater discharge, and that transport within the subsurface itself can be controlled by buoyancy-driven free convection.