Marine microfossil records from the Arabian Sea (AS) are mainly limited to foraminifera, with scanty information on other phyto- and zoo-plankton remains. Calcareous dinoflagellate cysts are one of the rarely studied microfossil groups across the world. In the present study, a calcareous dinoflagellate cyst (dinocyst) record from the eastern Arabian Sea (Off-Goa (SC-26)) during the Holocene is presented. Coccoides (vegetative stage of calcareous dinoflagellates) of Thoracosphaera heimii, Leonella granifera shows a dominance of 82–92% of the total assemblage suggesting a eutrophic environment throughout the studied period. The relative percentage of the dominant species T. heimii and L. granifera shows an opposite trend. The high relative abundance of Calciodinellum species during the early Holocene (prior to 10 ka BP) indicates a comparatively warm and low productivity environment compared with the late Holocene. A strengthening trend in the monsoon during the Holocene since 10 ka BP is reflected by the gradual increase in L. granifera, which is a runoff/terrestrial nutrient indicator. The high relative abundance of L. granifera, eutrophic taxa, and TOC since 6 ka BP reveals high primary productivity during middle to late Holocene compared with the early Holocene in the eastern Arabian Sea. Sand % which reflects runoff and L. granifera records show high similarity revealing that L. granifera % can be used as a terrestrial nutrient indicator, which has been suggested previously in studies from the Mediterranean Sea and South Atlantic. This record reveals the potential of calcareous dinoflagellate cysts to reconstruct monsoon variation, particularly runoff changes, in the Arabian Sea.