Seven oceanographic expeditions were conducted between the years 2013 and 2018 to determine the horizontal and vertical distribution schemes in the epipelagic and mesopelagic copepod community structure of the Caribbean Oceanic ecoregion (CAO) and the oceanographic variables that regulate it. Four indicator species are suggested for the North Equatorial Current and the Caribbean Surface Water (CSW) mass (Clausocalanus furcatus, Oncaea venusta, Temora stylifera and T. turbinate) and two indicator species for deep-water masses such as the Western North Atlantic Central Water (NACW) and the Antarctic Intermediate Water (AAIW) (Mormonilla phasma and Conaea rapax). The copepod assemblage responds to local oceanographic patterns that are regulated (24%) by the variability of dissolved oxygen and temperature in the water column. The horizontal structure of the copepod assemblage in offshore waters presented a spatial sectorization. Three zones were differentiated: (1) oceanic Colombian zone; (2) influence of the Magdalena River zone; and (3) offshore north-east zone. Water mass mixing processes and migration mechanisms favour the homogeneity of the vertical assemblage of copepods in the CAO ecoregion. This study provides relevant information on the structure and density of copepod species, providing key information to describe the ecological processes and the different responses to the oceanographic factors that modulate them.