Persistence of lipophilic toxins in different environmental compartments determines the way in which their concentrations can be used to evaluate temporal trends and associated risks. Short term stability of two lipophilic toxins, representing two chemically different groups of toxins — okadaic acid (OA) (Diarrhetic Shellfish Poisoning toxin) and 13-desmethyl spirolide C (13desmSPXC) (cyclic imine) — in seawater, interstitial water and sediment were analyzed. OA was found to be very stable in seawater, interstitial water and sediment, without significant changes over a 23-day period. Contrarily, 13desmSPXC was readily degraded, but faster in interstitial water than in seawater. In sediments, its degradation was also fast and dependent on the origin of the samples. 13desmSPXC was found in natural sediments, and this toxin was mostly associated to large particles (>10 μm) in the sediment, that are or include resting cysts of the producer species. Therefore, it appears that high concentrations of 13desmSPXC in seawater would indicate recent blooms of the producer species, while those of OA could be due to recent blooms or to others that took place long before detection. The absence of OA and 13desmSPXC indicates a low impact of those toxins in the study area.