Phycotoxin risk in the South China Sea is commonly assessed through harmful algal bloom occurrence, toxic phytoplankton abundance, and toxin concentrations in shellfish. However, this approach can underestimate exposure in subtropical coastal waters, where toxigenic species may remain at low abundance, toxins persist after release from algal cells, and contamination is transferred among environmental compartments and food webs. This presentation integrates recent studies of paralytic shellfish toxins (PSTs), lipophilic marine phycotoxins (LMTs), and domoic acid (DA) to examine the connected pathway from toxin production to environmental persistence, trophic transfer, seafood contamination, and ecological effects.In Daya Bay, PSTs were detected in phytoplankton and shellfish despite low densities of potential producers. By combining microscopy, 18S rDNA metabarcoding, clonal isolation, phylogenetic analysis, and toxin-profile comparison, Alexandrium pacificum was identified as the dominant source of C1/2 toxins. Matching toxin profiles among cultured isolates, field phytoplankton, and shellfish established a direct producer-to-seafood linkage. Yet algal abundance did not consistently reflect toxin levels, demonstrating that cell counts alone cannot reliably predict exposure because shellfish can accumulate and biotransform toxins over time.This limitation becomes clearer when phycotoxins are considered environmental contaminants rather than solely intracellular algal metabolites. Surveys across eutrophic estuaries and semi-enclosed bays revealed widespread LMTs in South China Sea seawater. Okadaic acid, dinophysistoxin-1, and pectenotoxin-2 were prevalent, especially in warm, wet-season waters and hydrodynamically retentive coastal settings. Dissolved and particle-associated toxins may therefore form an environmental reservoir, prolonging exposure after episodic toxic-algal production and linking seawater with suspended particles, sediments, and benthic organisms.A similar process-based framework explains DA risk in the Pearl River Estuary. Integrated pigment analysis, microscopy, ITS1 metabarcoding, LC-MS/MS quantification, and culture validation identified Pseudo-nitzschia cuspidata Clade III as the principal DA producer. Its proliferation and toxin production were favored by warm, saline summer conditions and nutrient stoichiometry rather than high nutrient concentrations alone. Although Pseudo-nitzschia remained below conventional bloom thresholds, DA was transferred from phytoplankton to zooplankton, crustaceans, and mollusks. Scallops accumulated up to 24.1 mg kg−1 DA, exceeding the Chinese regulatory threshold.  Future monitoring should integrate molecular source tracking, multi-media toxin measurements, food-web assessment, and ecological endpoints to detect hidden risks and support ecosystem-based management.