From an ecosystem management perspective, analysis of the functional roles of species is a challenge. It is valuable to determine which species are irreplaceable within a given community based on their contribution to the system’s organization. This study relates the emergent functional and structural indices of biological groups estimated from a trophic model of the Northern Gulf of California to identify the roles of these groups in the ecosystem context, with a particular focus on the role of the vaquita, an endemic porpoise in critically endangered status. The simulation of removing each group allowed the analysis of the removal’s functional effect on the ecosystem’s global attributes and organization (based on Ulanowicz’s ascendency concept). Groups from lower trophic levels (TL) were more related to complexity indicators, suggesting their contribution to the organization and structure of energy flows in the food web. Groups from intermediate TL had higher values of structural indexes, indicating their function in the control of flows throughout the network. The vaquita along with other marine mammals, aquatic birds, and some species of fish with a high TL contribute in a similar way to the order (for example, ascendency/capacity-of-development ratio) of the system, showing a relatively high value of ascendency (contribution of the group to the organization inherent to the ecosystem) and the change in ecosystem ascendency when they were removed. The vaquita, like marine and coastal birds, plays a small role in the ecosystem. But like them, it does contribute substantially to ecosystem organization. This study thus provides information potentially useful for management in understanding the species’ role and in reducing uncertainty in decision-making.