Ecosystem-based modeling is rapidly becoming an established technique to investigate the health and stability of ecosystems. In the Gulf of Mexico, ecosystem models are applied to neritic systems, but less focus has been placed on the oceanic domain. Since 2011, severe declines have been observed in many micronekton groups that occupy the mesopelagic zone (200 – 1000 m depth). Here we present an ecosystem model for the oceanic northern Gulf of Mexico for the year 2011, simulate that model according to micronekton trends through 2018, and quantify the top-down and bottom-up impacts that each functional group has on one another. These trends were examined to determine whether interactions between the two groups have changed directionally over time. In 2011, zooplankton (trophic level =2) occupied greater than one-third of the total metazoan biomass, and also 40% of the total energy throughput ascended to higher trophic levels in the system. Of the 1849 possible functional group interactions (most of which are indirect), approximately 27% showed significant changes between 2011 and 2018, which were related to shifts in biomass and diet throughout the simulation. Direct top-down interactions changed more frequently than other types of trophic relationships. The frequency of direct changes that occurred in the simulation was not observed evenly among all functional groups, as opposed to indirect interactions. These changes between functional group interactions can be used to further examine potential shifts in the trophic structure of marine ecosystems under various forcing scenarios.