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Abstract Islands in the tropical Pacific supply elevated nutrients to nearshore waters that enhance phytoplankton biomass and create hotspots of productivity in otherwise nutrient‐poor oceans. Despite the importance of these hotspots in supporting nearshore food webs, the spatial and temporal variability of phytoplankton enhancement and changes in the underlying phytoplankton communities across nearshore to open ocean systems remain poorly understood. In this study, a combination of flow cytometry, pigment analyses, 16S rRNA gene amplicons, and metagenomic sequencing provides a synoptic view of phytoplankton dynamics over a 4‐yr, near‐monthly time series across coastal Kāneʻohe Bay, Hawaiʻi, spanning from an estuarine Indigenous aquaculture system to the adjacent offshore environment. Through comparisons with measurements taken at Station ALOHA located in the oligotrophic North Pacific Subtropical Gyre, we observed a sharp and persistent transition between picocyanobacterial communities, fromSynechococcusclade II abundant in the nearshore toProchlorococcushigh‐light adapted clade II (HLII) proliferating in offshore and open ocean waters. In comparison to immediately adjacent offshore waters and the surrounding open ocean, phytoplankton biomass within Kāneʻohe Bay was dramatically elevated. Members of the phytoplankton community revealed strong seasonal patterns, while nearshore phytoplankton biomass positively correlated with wind speed, rainfall, and wind direction, and not water temperatures. These findings elucidate the spatiotemporal dynamics underlying transitions in ocean biogeochemistry and phytoplankton dynamics across estuarine to open ocean waters in the tropical Pacific and provide a foundation for quantifying deviations from baseline conditions due to ongoing climate change.