The vertical thermohaline and biogeochemical structures of the upper layer (0 - 200 m) were studied in the Gulf of Tadjourah using high-resolution hydrographic data collected in July-August 2013, September 2013 and February 2014. During summer, the superficial layer consisted of the mixed layer (ML) extending to a depth of about 20 - 30 m followed by the thermocline located between 30 and 50 m depth. The ML was thicker in the west and the southeast where the thermal gradient and chlorophyll a concentrations were particularly high. During September, this stratification persisted but the ML became warmer and saltier and the thermocline moved slightly deeper. In February, the ML extended to about 120 m, and the thermocline was less pronounced. A comparison of the directly measured currents to the wind induced Ekman current and to geostrophic velocity profiles revealed that the thermohaline and the biogeochemical features in summer were related to the southwest monsoon (SWM). The SWM drives surface water from the Gulf of Tadjourah to the Gulf of Aden and thus induces westward intrusion of the high salinity thermocline water from the Gulf of Aden; this near surface flow mixes surface waters in the extreme west of the Gulf of Tajourah. In contrast, the northeast monsoon (NEM), predominant in winter, brings cold water toward the Gulf of Tadjourah and thickens the ML through convective mixing. Our study shows that the SWM plays a crucial role in the stratification of the water column during summer but bathymetry influences its effects. The bowl-shape of the basin and its elongated slope in the west enhance the upwelling in this area where negative sea surface temperature anomalies and high chlorophyll a concentrations were observed.