This study examines the environmental conditions and hydrographic dynamics in Tawi-Tawi within the Sulu Archipelago, a region influenced by the interplay of distinct water masses from the cooler, saltier Sulu Sea and the warmer, fresher Celebes Sea. Pronounced spatial gradients in sea surface temperature and salinity were observed; however, these hydrographic patterns did not correlate directly with Chl a concentrations or microbial plankton biomass, indicating that biological productivity is more strongly governed by current velocity and tidal dynamics. Spectral analysis confirmed tidal currents as the dominant driver of water transport, explaining over 95% of the variability in the region. Tidal currents can induce horizontal advection and retention zones on the shallow (<200 m) bathymetric shelves around Bongao, Sibutu, and Sitangkai, which promote plankton aggregation and enhanced nutrient mixing. Baroclinic tides were generated by the interaction of barotropic tides with complex bathymetry, such as in Sibutu and Sitangkai. This interaction produces internal waves that support vertical nutrient flux and persistent upwelling, enriching surface waters as evidenced by elevated Chl a and microbial density in Tawi-Tawi. Sampling during highest high water further intensified vertical mixing, nutrient availability, and horizontal advection, collectively elevating picoplankton and virioplankton abundance. The microbial community was dominated by viruses and heterotrophic bacteria, but Synechococcus prevailed among the autotrophs due to its high adaptability to dynamic mixing conditions. The spatial heterogeneity in microbial populations reflects the combined influence of physical transport processes and the ecological tolerances of plankton, underscoring the complexity of biological productivity regulation in this archipelagic system