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Mandovi and Zuari estuarine complex is monsoon-influenced estuaries located along the central west coast of India. During the past few years, there has been an increase in nutrient loading specially during monsoonal runoff which is responsible for the growth of harmful algal flora. To understand occurrence and distribution of harmful algal blooms species, daily/alternate day samplings were carried out in Mandovi and Zuari estuaries during 2007-2008 and 2008-2009 periods, respectively, comprising of monsoon (June–November) and nonmonsoon (December–May). In Mandovi, total 54 HAB species with 49 in monsoon and 36 during nonmonsoon period were reported. In Zuari, total 46 HAB species with 38 in monsoon and 41 were reported during nonmonsoon period. Bray-Curtis cluster analysis based on log-transformed phytoplankton density detected seven well-defined groups revealing spatiotemporal variability. The density of the dominant harmful algal species was significantly positively correlated with nutrients, but negatively correlated with salinity. The results of the study indicate that monsoon plays an important role in occurrence and distribution of harmful algal species having direct correlation with salinity variations and nutrient loading.