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Phytoplankton are important components of coastal marine ecosystems that are strongly influenced by freshwater inputs from land, including submarine groundwater discharge (SGD). Although SGD generates sharp onshore - offshore gradients in physical and chemical conditions at several locations around Hawaii Island little is known about the biotic responses of water column microbes to these conditions. We studied the distributions of phytoplankton and bacteria at two contrasting sites with SGD-fed fishponds, Kiholo and Kaloko Bay, including the full range of salinity extending from the fishponds to the coastal ocean. We addressed the hypotheses that (1) SGD-fed fishponds support a higher biomass and different composition of phytoplankton than the adjacent ocean, and (2) phytoplankton biomass and composition are related to SGD-driven salinity gradients in the coastal ocean. Phytoplankton biomass in fishponds was elevated (10-100-fold) and accompanied by higher average cell size pico- and nano-phytoplankton (2-6 mu m) relative to sites outside the fishpond. General additive models (GAMs) showed elevated biomass and average cell size at mid-range salinities and declining biomass at salinity < 20 outside the fishponds. Multivariate RDA showed significant, site-specific relationships between surface phytoplankton biomass (Chl a), cell counts, and environmental parameters. Analysis of surface vs. deep samples from outside the fishponds showed elevated phytoplankton biomass at the surface, except in Kiholo lagoon where phytoplankton was elevated beneath the SGD-driven pycnocline. This study shows structuring of coastal phytoplankton through SGD inputs and suggest that changes in SGD due to coastal development or climate change can impact coastal marine ecosystems through effects on phytoplankton communities.