Seasonal blooms of Pseudo-nitzschia spp., along with corresponding seasonal increase/decrease in domoic acid concentrations, consistently occur in the waters surrounding the Santa Cruz Municipal Wharf. Domoic acid has been intermittently observed in the water column when Pseudo-nitzschia spp. are not present, and presence or absence of cells is generally a poor indicator of toxin concentration in the water and sentinel mussel samples. Chlorophyll a and domoic acid values from seawater, sediment and Solid Phase Adsorption Toxin Tracking (SPATT) samples from February through December 2013 were analyzed and compared to a long-running weekly time series at the Santa Cruz Municipal Wharf, part of the California Department of Public Health monitoring program, to investigate retention of domoic acid in the sediments. We hypothesized that domoic acid concentrations in the sediment would increase immediately following a Pseudo-nitzschia bloom and increased domoic acid concentrations in the water column would follow a mixing event due to sediment and bottom water resuspension. Despite the lack of a significant toxic algal bloom during the study period, domoic acid was consistently observed at the sediment-water interface. Peaks of domoic acid concentrations in SPATT samples preceded peaks of particulate domoic acid from seawater samples, suggesting that the domoic acid source was more closely associated with the sediment-water interface. Sediment resuspension is a likely origin, suggesting that the sediment is potentially acting as a reservoir for domoic acid. It may be important for public health monitoring programs to include a sediment toxin analysis, particularly given the known presence of domoic acid in commercially harvested benthic organisms, such as crabs and flatfish.