Time series of shipboard observations in the southern Arafura Sea near the Tiwi Islands indicated that the water column dynamics differed between the east and west sides of the islands. On the west side, the water column, characterized by temperature, salinity, and velocity, was barotropic and tidal advection dominated. On the east side, the water column was baroclinic and internal tides were present along with tidal advection. These conditions affected the distribution of the turbidity and fluorescence in the water column. Likewise, the influence of the daily solar radiation cycle reached the bottom on the western side, but was limited to the upper layer above the thermocline on the eastern side. The fluorescence peaks also differed between the east and west sides, with the eastern side dominated by the semidiurnal tides and the western side by the daily solar cycle. Fluorescence integrated over the water column was much higher on the eastern side than the western side. Also on the eastern side, fluorescence was limited to the lower layer, while on the western side, it encompassed the entire water column at times and peaked below the warmer, higher oxygenated water generated by solar radiation and surface mixing. These dynamics have distinct implications for biological productivity and also may affect a proposed tidal power system in the region.