Physical oceanography variables and carbon flux (for juveniles/adults of dominant mesopelagic migratory species) were determined during the CAPEGOLCA XIII and CAPEGOLCA XIV cruises (June-October 2018). This dataset contains the depth, temperature, and conductivity that were recorded with a Star-ODDI CTD attached to a Bongo net during CAPEGOLCA XIII and with a SeaBird SB11 CTD attached to an oceanographic rosette in CAPEGOLCA XIV. Values of numerical abundance, migrant biomass, specific respiration and respiration flux data for each individual of fishes, decapods and large euphausiids analyzed at the north-central regions in the Gulf of California are given. Specimens were collected during the nighttime (20:00–05:00 h local) using a standard Bongo net (0.61 m mouth diameter, 505 µm mesh net). The integrated layer from maximum depth to surface (32–272 m) was evaluated through oblique hauls for each cruise. Collected specimens were identified on board to the lowest possible taxonomic level and those selected for electron transfer system (ETS) activity analysis were immediately frozen in liquid nitrogen contained for posterior chemical analyses in the land-based laboratory. Values of abundance, migrant biomass, specific respiration and respiration flux were integrated from sampling depth to surface.