To date, understanding the fate of lipophilic marine algal toxins (LMATs) in benthic environments on which cultivated shellfish depend is still limited. In this work, the occurrence, concentration levels, and phase distributions of LMATs in the benthic environments of two mariculture sites (Sishili and Rongcheng Bays) in China were investigated for the first time. Five LMATs: okadaic acid (OA), pectenotoxin-2 (PTX2), gymnodimine, 13-desmethyl spirolide C, and azaspiracid-2 (AZA2) and three derivatives: dinophysistoxin-1 isomer (DTX1-iso), pectenotoxin-2 seco acid, and 7-epi- pectenotoxin-2 seco acid were detected in different environmental samples. OA and PTX2 were the dominant LMATs in the bottom boundary layer (BBL) and sediment, whereas AZA2 was present in the sediment only. Notably, DTX1-iso was found for the first time to be widely distributed in the benthic environments of the bays. In BBL, the average proportion of LMATs in the dissolved phase (99.20%) was much higher than in the particulate phase (0.80%). Partition of LMATs was more balanced between sediment porewater (57.80% average proportion) and sediment (42.20%). The concentrations of ∑LMATs in the BBL seawater ranged from 19.09 ng/L to 41.57 ng/L (mean of 32.67 ng/L), and the spatial distribution trend was higher in offshore than nearshore. ∑LMATs concentrations in the sediment and porewater of the two bays ranged from 17.04 ng/kg to 150.13 ng/kg (mean of 53.58 ng/kg) and from 8.29 ng/L to 120.58 ng/L (mean of 46.63 ng/L), respectively. Their spatial distributions differed from those in BBL, showing a trend of high concentrations in areas with heavy land-based inputs. ∑LMATs concentrations in porewater were significantly higher than those in BBL seawaters, suggesting that the potential hazards of LMATs to benthic organisms may be underestimated.