Chlorophyll-a (Chl-a) is widely regarded as a proxy for phytoplankton biomass. In marine environments, the concentration of Chl-a and its vertical and horizontal distributions are closely linked to the water column hydrography and nutrient availability. This study aimed to assess the spatial distribution of Chl-a in the deep waters of the southern Gulf of Mexico and evaluate its relationship with hydrography and nutrient concentrations during the summer season. A multidisciplinary research cruise was conducted in August and September 2018 to collect high-resolution hydrographic data and water samples at various depths (surface, 10, 20, 50, 100, and 150 m). These samples were analyzed for nutrient content and Chl-a concentration. The results revealed significant horizontal and vertical variability. Notably, a low-temperature, high-density core was identified at 50 m depth, indicating the presence of a cyclonic eddy. Within this cold, dense core, nutrient levels increased, while Chl-a concentrations peaked at depths of 50 m and below. Principal Component Analysis confirmed that temperature and nutrients were the primary drivers of Chl-a concentrations, particularly at 50 m depth, and below. While previous research has explored Chl-a distribution in the southern Gulf of Mexico, few studies have used in situ observations to examine deeper regions. This study demonstrates how hydrographic conditions regulate nutrient and Chl-a dynamics in an area where deep-water sampling remains operationally and economically challenging.