Toxic phytoplankton blooms threaten coastlines worldwide by diminishing beach quality and adversely affecting marine ecosystems and human health. The common diatom genus Pseudo-nitzschia consists of several species known to produce the neurotoxin domoic acid. Recent studies suggest that algal blooms dominated by Pseudo-nitzschia are increasing in frequency and duration owing to changes in coastal nutrient regimes. However, few studies have examined the persistence or long-term biogeochemical cycling of domoic acid in marine waters. Here, we measure the concentration of domoic acid in surface waters and sediment traps—up to 800?m in depth—off the coast of Southern California. We show that peaks in Pseudo-nitzschia abundance and domoic acid concentrations in surface waters coincide with peaks in diatom and toxin abundance at depth, suggesting rapid downward transport of the toxin. In some cases, the sinking particles contain over five times the United States federal limit of domoic acid. Detection of domoic acid in bottom sediments indicates that the toxin may persist long after the Pseudo-nitzschia blooms. Our results indicate that vertical fluxes of domoic acid are a substantial source of the toxin to deep-ocean food webs, and could explain high levels of domoic acid previously observed in benthic organisms.