Subsurface chlorophyll maxima (SCM) are a prominent feature of oligotrophic oceans, reflecting the complex interplay between physical stratification, nutrient availability, and phytoplankton adaptation. Despite the ecological importance of the Red Sea, the spatial variability and physical controls governing SCM remain insufficiently understood. This study investigated the hydrographic and biogeochemical characteristics associated with SCM in the Red Sea using in situ observations collected during winter surveys in 2012, 2013, 2014, and 2015. A series of cross-basin transects were analyzed to examine the vertical and horizontal distributions of chlorophyll-a (Chl-a), temperature, salinity, density, dissolved oxygen, and Brunt–Väisälä frequency. In addition, spatial distributions of hydrographic and biogeochemical properties at 75 m and 400 m depth were examined to characterize intermediate water masses and their relationship with phytoplankton distribution. To place the observations within a basin-scale dynamical framework, HYCOM-derived hydrography and circulation fields were also analyzed. All transects consistently revealed a well-stratified upper water column with a pronounced subsurface chlorophyll maximum. The SCM was closely associated with intermediate density layers located beneath the seasonal thermocline, where enhanced water-column stability and favorable hydrographic conditions support phytoplankton accumulation. Temperature–salinity characteristics indicate that evaporation-driven salinity enhancement, strong vertical stratification, and intermediate-layer mixing are the primary processes shaping the hydrographic structure of the northern Red Sea. HYCOM simulations further demonstrate persistent northward intermediate-layer transport, pronounced mesoscale eddy activity, and subsurface intrusions that collectively influence water-mass transformation, nutrient transport, and the spatial variability of biological productivity. The close correspondence between SCM distribution, thermohaline structure, and basin-scale circulation highlights the critical role of physical processes in regulating phytoplankton biomass in the oligotrophic Red Sea. These findings provide new observational evidence of the mechanisms controlling SCM formation and persistence and improve our understanding of physical–biological coupling in one of the world's warmest and most nutrient-limited marine ecosystems.