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ABSTRACT Harmful algal blooms (HABs) can negatively affect coastal water quality, aquatic fauna, and human health from the consumption of toxin-contaminated seafood. Estuaries are especially prone to the incidence of these noxious events and sensitive to the associated damage. This study represents a comprehensive overview of previous investigations reporting the occurrence of harmful algae and/or phycotoxins in the Paranaguá Estuarine Complex (CEP), in Southern Brazil. Secondary data from 2002 to 2021 were combined with new results obtained from widely spaced sampling campaigns performed from 2018 to 2019 to assess the periods and estuarine sectors at greater risk for the incidence of HABs. In total, about 600 water/sediment samples containing harmful microalgae and 675 tissue samples of phycotoxin-contaminated fauna were analyzed. The most frequent and abundant species of potentially toxic microalgae were dinoflagellates belonging to the species complexes Dinophysis acuminata and Prorocentrum lima, producers of diarrhetic shellfish toxins (DSTs), and diatoms of the genus Pseudo-nitzschia, producers of amnesic shellfish toxins (ASTs). Okadaic acid, a DST, was by far the most common toxin in the fauna, reaching higher levels in primary consumers such as bivalve mollusks (mussels, oysters, and clams), zooplankton, and suspension-feeding crustaceans (ghost shrimps), and moderate to low levels in cephalopods, fishes, gastropods, echinoderms, sea turtles, seabirds, and cetaceans. Less rainy periods (winter-early spring) were associated with the highest incidence of DSTs and blooms of their producing algae P. lima and Dinophysis spp., mainly in the middle region of Paranaguá Bay and on the shallow continental platform adjacent to the estuarine mouth. However, certain HAB-forming species may be more successful in inner estuarine areas ( Prorocentrum cordatum) and during different periods, such as late summer—early fall ( Pseudo-nitzschia spp.). Continuous monitoring of harmful algae and toxins is therefore highly recommended to mitigate the effects of HABs in the entire estuary. (HABs quality toxincontaminated contaminated seafood damage andor or CEP, CEP , (CEP) Brazil 200 202 201 total 60 watersediment sediment 67 phycotoxincontaminated phycotoxin analyzed DSTs, (DSTs) Pseudonitzschia, Pseudonitzschia Pseudo nitzschia, nitzschia ASTs. ASTs . (ASTs) acid DST mussels, mussels (mussels oysters clams, clams clams) zooplankton suspensionfeeding suspension feeding ghost shrimps, shrimps shrimps) cephalopods fishes gastropods echinoderms turtles seabirds cetaceans winterearly winter early spring P spp spp. mouth However HABforming HAB forming cordatum summerearly summer spp.. spp.) estuary (CEP 20 6 (DSTs (ASTs 2