In order to trace the history of dinoflagellate cyst assemblages and provide new insights in to Harmful Algal Bloom (HAB) dynamics in monsoon‐influenced tropical environments, sediment cores were collected from four different coastal locations along the west coast of India. The naturally occurring radionuclide ²¹⁰Pb activity in the sediment samples were measured; and subsequently the sedimentation rates (SRs) and ages were modeled. The SRs ranged from 0.15±0.01 to 2.80±0.38 cm/yr and provided coverage of time period spanning between 21 and 145 yr. Cysts of potential harmful dinoflagellates (Gonyaulax spinifera, Lingulodinium polyedrum, Protoceratium reticulatum and Scrippsiella trochoidea) were observed to be present earlier than the 20th century. Among the four sediment cores, significant temporal variations in cyst abundance were observed in the sediment core, off Mangalore. Two of the cores from off Mangalore and Cannanore were dominated by autotrophic cyst assemblages (Gonyaulax membranacea and Gonyaulax spinifera) in the deeper sediment sections. However, the upper sediment sections were dominated by heterotrophic forms. Temporal shifts in cyst assemblages from autotrophic to heterotrophic dinoflagellates in the Mangalore core coincided with high deposition of shells; carbon analyses (δ¹³C_org and C_org:N ratio) revealed shifts in organic matter type from terrestrial to marine source. The terrigenous input in this region, influenced by the monsoonal variations, can thus affect dinoflagellate assemblage structure and lead to changes in ecosystem functioning.