<p>Seagrass meadows and coral reefs are interconnected habitats in many tropical coastal regions. Despite extensive studies, the overall impact of the seagrass-coral reef interaction on resident microscopic species remains underexplored. In this study, we investigated phytoplankton and benthic microalgal communities in seagrass meadow-coral reef ecosystem using mesocosms over six-week. We measured water quality, sedimentation, nutrient concentrations, chlorophyll a, and relative abundance of phytoplankton and benthic microalgae. Our results showed significantly higher silicate concentrations, chlorophyll a levels, and total sediment accumulation in seagrass mesocosms compared to controls. Biotic data showed that the phytoplankton community in seagrass mesocosms had an elevated relative abundance of symbiotic dinoflagellates (<i>Symbiodinium</i>), whereas the benthic microalgal community showed a higher relative abundance of dinoflagellates (<i>Prorocentrum</i> sp., <i>Alexandrium</i> sp., and <i>Cochlodinium</i> sp.) that were historically associated with toxin production. Elevated abundance of free-living <i>Symbiodinium</i> in seagrass mesocosms, along with increased nutrient concentrations, suggests a potential risk to coral-algal symbiotic stability. While high nutrient concentrations can increase benthic algal productivity, carbon sequestration, and provide food for diverse organisms, the presence of seagrass may create conditions favorable to the growth of potentially harmful dinoflagellates, although these taxa accounted for less than 7% of the total benthic algal community.</p> Graphical Abstract <p></p>