The Haruku Strait, on the Maluku Islands, Indonesia, lies between Haruku, Pombo, and Ambon Islands, forming a dynamic marine passage. This study analyzed the physical characteristics and stratification of water masses during the Southeast Monsoon (August–September 202 2) to understand their role in nutrient distribution, heat dispersion, and circulation. Due to its geographic and oceanographic conditions, the strait is an ideal site to examine monsoon-driven mixing processes. Data were collected at 16 stations across multiple depths using a CTD Rinko ASTD 101, measuring temperature, salinity, and density. Results showed significant vertical and horizontal variations. In August, peak upwelling in the Banda Sea and strong Southeast Monsoon winds led to notable changes in water characteristics. By September, both upwelling and wind intensity weakened, reducing stratification differences. Water mass analysis identified North Pacific Subtropical Water (NPSW) in the thermocline layer at all depths. Stratification analysis using Brunt-Väisälä frequency (N²) calculations indicated higher stability in the thermocline layer, with N² values greater than those in surface layers across the northern, central, and southern regions. These findings highlight the seasonal monsoon's influence on water mass stratification, emphasizing its role in sustaining marine ecosystems under varying monsoon intensities.