A multibeam sonar combined with an Acoustic Doppler Current Profiler (ADCP) were used at the Veracruz Reef System (VRS), Gulf of Mexico, during the spawning period of August 2016 in order to elucidate plankton trajectories within the study area. The new high-resolution bathymetry provided the location of 50 coral reefs, 27 more reefs than known at the VRS. Most of those reefs are submerged reefs located at depths greater than 40 m. The total coral reef area of the VRS was calculated in 70.1557 km2. Only ~10% of the total area corresponds to submerged reefs. Forty-eight species were identified, seven more than known species at the VRS, 45 of the order of Escleractinia and 3 of the order of Anthoathecatae. Acropora prolifera, a hybrid, was also identified in most reefs. All species were observed in the emerged and submerged reefs. The distance at which the three local river discharges (Jamapa, La Antigua, and Actopan) brought sediments to the VRS was calculated. Those are inappropriate areas for coral settlement or development due to sediment transport and temperature and salinity fluctuation. Finally, light penetration was measured at 19 m depth near one reef structure during August 2016 suggesting that even during cloud coverage and rain periods there was a light bioavailability at the sampling point.