While fishing discards and bycatch are worrisome for fisheries management, research has been mainly focused on commercial or threatened species, while the ecosystem effects were largely neglected. In this work, the effects of discard and fishing efforts on the structure and the functioning of the food web of the Río de la Plata (RdlP) were analyzed using mass balance and dynamic trophic modeling. Discard is consumed almost entirely by several species with a large preference for it, producing mixed trophic impacts. The role of discard on the global attributes of the RdlP ecosystem does not seem important, resulting in a low incidence in trophic flows, growth, and development of the trophic web. Dynamic simulations showed a mixed response to variations of discards, with some groups responding positively and others negatively. For example, a decrease in discards would produce a slight decrease in the biomass of most functional groups, being more pronounced in the predators of the system. Variations in biomass produced by discards are more sensitive under the assumption of bottom-up ecosystem control than mixed control and to a lesser extent under top-down control. Our work confirms a complex relationship between discards and ecosystem functioning, warning about the beneficial result of discard reduction policies.