Abstract Indonesian Through Flow (ITF) forms unique water mass characteristics in Indonesian Marine Waters. This water mass enters through the Makassar Strait into the Banda Sea by crossing the Flores Sea. This study aims to analyse the characteristics of water masses in the Flores Sea during the transition season. In situ data was obtained using conductivity temperature depth (CTD) at four stations in the Flores Sea from April to May 2023. Next, the data was processed and analysed for layer thickness through vertical stratification and water mass characteristics using T-S diagrams. The analysis results show that the thickness of the homogeneous layer in the Flores Sea in the first transition season is between a depth of 0-40 m, the thermocline layer is at a depth of 40-300 m, and the depth layer is from a depth of 400-900 m. Apart from that, the characteristics of the water mass identified through the T-S diagram are: North Pacific Subtropical Water (NPSW) is found at a depth of 100-150 m with a temperature between 20-26° C and a salinity between 34.9-35.4 psu. Another water mass is South Pacific Intermediate Water (SPIW) at a depth of 500-800 m with a temperature of 6-8° C and a salinity of 34.55-34.65 psu. In contrast, the Antarctic Intermediate Water (AAIW) was found at a depth of >750 m with a temperature of 5-6° C and a salinity of 34.5-34.6 psu.