This study investigates the contribution of several marinas to fecal indicator bacteria impairment in Newport Bay, a regionally important tidal embayment in southern California. Three different fecal indicator bacteria groups were assayed, including total coliform, Escherichia coli, and enterococci bacteria, all measured using the IDEXX Colilert and Enterolert system. To document temporal variability in the fecal indicator bacteria signal, water column samples (n = 4132) were collected from two marinas over time scales ranging from hours to months. To document spatial variability of the fecal indicator bacteria signal, water column and sediment samples were collected from a number of sites (n = 11 to 36, depending on the study) in and around the two marinas, over spatial scales ranging from meters to kilometers. To identify the dominant temporal and spatial patterns in these data a statistical approach--Empirical Orthogonal Function analysis--was utilized. Finally, to clarify the transport pathways responsible for the observed temporal and spatial patterns, fecal indicator bacteria data were compared to simultaneous measurements of tidal flow, temperature, and salinity. The results of this field effort collectively implicate runoff--both dry weather runoff at sampling sites located near some storm drains and wet weather runoff at all sites--as a primary source of fecal indicator bacteria in the water column and subtidal sediments. The results and analysis presented here reinforce the growing body of evidence that management of fecal indicator bacteria impairment in the coastal waters of southern California will require developing long-term strategies for treating nonpoint sources of both dry weather and stormwater runoff.