Plankton communities are influenced, in part, by water exchange with adjacent estuarine and oceanic ecosystems. Reduced advective transport through tidal passes or with adjacent bay systems can affect chemical processes and biological interactions, such as nutrient cycling, phytoplankton abundance and productivity, community respiration, and zooplankton biovolume. The most threatened estuarine ecosystems are shallow, bar-built, microtidal estuaries with small water volumes and restricted connections through tidal passes and other water exchange points. This research explored spatio-temporal trends in plankton communities and the physicochemical environment in Mesquite Bay, Texas a microtidal, bar-built, subtropical estuary in the Gulf of Mexico. This research couples sampling at fixedstations for multiple physical and biological parameters with high-resolution spatial mapping of physicochemical parameters. Spatial trends were less in magnitude and affected fewer parameters in fixed station and spatial data. Two dimensional ordination plots indicated spatial heterogeneity with a more pronounced temporal trend affecting parameters including temperature, salinity as a function of inflow timing, and seasonal wind direction affecting primary production and zooplankton biovolume. Temperature was positively correlated with gross production and respiration rates during spring and late summer with sporadic positive and negative correlations with phytoplankton biomass. The timing and magnitude of freshwater inflow affected various physicochemical and biological parameters. Higher than 71-year inflow rates resulted in low salinity system wide, with spatial heterogeneity increasing over the course of the study, which was confirmed by spatial maps. Additionally, high inflow rates led to two periods of increased inorganic nutrients and dissolved organic matter. Low salinity periods coincided with persistence of higher turbidity, likely because of decreased sediment flocculation. Gross production was low at this time, and likely from light limitation. Additionally, wind magnitude and direction created spatial heterogeneity in turbidity levels and phytoplankton biomass. Zooplankton biovolume was highest during spring and late summer with high species diversity in total rotifers. Copepod biovolume and phytoplankton biomass were positively correlated. Other zooplankton taxonomic groups exhibited variable correlations with phytoplankton biomass and other taxonomic groups. Further long-term studies are needed to determine interactions of various components of trophic food-webs and account for interannual variability in all system parameters.