Plankton communities are important members of the food web in coastal systems and are regulated by top-down and bottom-up controls. This study examined the influence of bottom-up controls, such as physicochemical factors, and top-down controls, such as predation, on the plankton communities in South Bay, Texas. Microalgal photopigments were ascertained by high-performance liquid chromatography (HPLC) to determine the relative abundances of major algal classes. Zooplankters were identified to the lowest possible taxon and enumerated. No spatial trends were observed for the physicochemical factors. The northern bay sections exhibited significantly higher phytoplankton and microphytobenthic diatom biomass, probably due to their proximity to the bay inlet. Copepod, gastropod veliger and brachyuran zoea abundances were also higher in this area, albeit insignificantly. The southern bay sections experienced significantly higher cyanobacterial, euglenophyte and chlorophyte biomass, and polychaete larval abundances. Total zooplankton and nauplii abundances were also higher in the southern areas, albeit insignificantly. Sampling the inaccessible areas of the bay in the future may reveal spatial variability among the physicochemical factors which could be influencing the distribution of plankton. Temporal variation for the physicochemical factors followed a typical trend for subtropical climates and influenced the seasonality of the plankton communities. Phytoplankton biomass peaked in February, August and October but these maximums were not significantly different from the other months sampled. Microphytobenthic biomass peaked during the summer months, while diatom biomass also peaked in February. Zooplankton abundances peaked in October, while nauplii and polychaete larvae also peaked in February. Relationships between wind speed, turbidity and the microalgal pigments were assessed to determine if wind-induced resuspension influenced the location of the major algal classes within the water column compared to the sediments. Wind speed and turbidity were directly related to each other, albeit insignificantly. Some phytoplankton and microphytobenthos were considered tychopelagic because wind-induced resuspension increased their biomass in the water column compared to the sediments. The physicochemical factors exerted bottom-up control of plankton community dynamics in this study, while top-down controls, such as predation, require further investigation. Future studies should focus on which of these controls have more influence on plankton community dynamics in South Bay.