Food web dynamics consist of processes that affect ecosystem structure and functioning. EcoTroph (ET) is a recently developed approach and software for modeling aquatic ecosystems, articulated entirely around the trophic level concept. Here, we used ET to investigate impacts of 2 trophic controls (i.e. foraging arena and top-down controls) on marine ecosystem trophic flows and associated fishing effects. A new version of the ET model accounting for the foraging arena theory was developed. Cross impacts of the 2 trophic controls and different fishing scenarios were analyzed using a virtual ecosystem. Results showed that foraging arena controls decreased the resistance and production of an ecosystem facing increasing fishing mortality. In contrast, the inclusion of top-down controls resulted in a more resistant ecosystem, with a decrease in the kinetics of trophic flows at lower trophic levels (TLs) when the abundance of higher TLs is reduced by fishing. These 2 controls increased the interactions between TLs, and, in part, shaped fishing impacts at the ecosystem scale. Then, we applied ET to 3 real ecosystems which have been previously modeled using Ecopath with Ecosim (EwE). EcoTroph and Ecosim predictions related to changes in fishing effort were compared, and showed that accounting for trophic controls enabled EcoTroph to mimic Ecosim models, and better reflect associated changes in trophic flows. The 3 case studies exhibited different behaviors: while the pelagic ecosystem had strong foraging arena controls but no top-down controls, the other ecosystems were characterized by weaker foraging arena controls but effective top-down controls.