Ocean eddies play a major role in lateral and vertical mixing processes of particulate organic carbon (POC), as well as in the transport of heat, salinity, and biogeochemical tracers. In the open waters of the Gulf of Mexico (GoM), however, there are limited observations to characterize how these mesoscale structures affect the spatial distribution of POC in the upper water column, and its importance for organic matter cycling and export. We present the distribution patterns of POC relative to mesoscale features from surface waters in the deep-water region of the GoM during three oceanographic cruises held during the summer months of 2015, 2016, and 2017. Samples were collected under well-stratified upper ocean conditions, which allowed us to assess the spatial and temporal distribution of POC as a function of non-steric sea surface height, density, apparent oxygen utilization, and chlorophyll fluorescence-a. We further explored the variability of integrated surface layer POC concentrations in stations located within the cores and the edges of cyclonic and anticyclonic eddies, or those collected outside these structures. Our results show how the mesoscale eddies influence several important physical and biogeochemical variables as well as the POC concentrations in the surface layer. POC concentration in the surface layer seems to be influenced depending on their locations in these mesoscale structures. Lower POC concentrations are consistently observed in the border of the cyclonic and the center of the anticyclonic eddies, in contrast to the higher POC concentrations observed at the center of the cyclonic and the border of anticyclonic eddies. These mesoscale processes are more prominent in the central part of the GoM and along the path of the large anticyclonic eddies detached from the Loop Current, implying the importance of mixing by mesoscale dynamics for the carbon production and export to depth in this oligotrophic deep-water region of the GoM during the strongly stratified summer season.