The Lakshadweep Islands, situated in the South Eastern Arabian Sea, exhibit unique hydrodynamic characteristics influenced by monsoonal variations and regional oceanographic processes. This study investigates the variability in hydrography and circulation within a shallow region of the islands, focusing on Agatti Island during the transition period (March–May 2019). High-resolution observations were conducted using a moored Acoustic Doppler Current Profiler (ADCP) and buoy-deployed sensors, capturing 45 days of continuous data on wind, tide, current, and temperature profiles. Results reveal moderate wind speeds averaging below 4 m/s, predominantly northeasterly, with notable diurnal variability in air and sea surface temperatures (SST). SST rose from 28.5 ℃ to 30.5 ℃ during the observation period, correlating with increased atmospheric heating. Currents displayed moderate amplitudes below 0.5 m/s, with strong tidal currents peaking at 15 cm/s. The mixed semidiurnal tide dominated, marked by pronounced spring-neap cycles. Barotropic and baroclinic currents were identified, the latter showing vertical structures indicative of internal tides and inertial oscillations. Subsurface temperature analyses highlighted significant heat accumulation influenced by vertical mixing and baroclinic activity, posing implications for coral reef ecosystems in a warming climate. These findings highlight the intricate interplay of atmospheric and oceanographic forces shaping the region’s hydrodynamics. Understanding these processes is crucial for assessing coral reef vulnerability and informing coastal management strategies in the context of global climate change.