In the late 1990s, depletion of the target species Penaeus notialis (Pink Shrimp) in deeper waters (50 m) of the Nigerian coast resulted in a change of target species from P. notialis (Pink Shrimp) to shallower water species such as Penaeus monodon (Brown Shrimp). This study investigates the hypothesis that ecosystem impacts increased as industrial fleets increased fishing in shallower areas of the Nigerian coast by comparing the state of the ecosystem before and 20 yr after commercial shrimping commenced in Nigerian coastal waters (NCW). Two fishing scenarios were developed in Ecospace, the spatial modeling module of Ecopath with Ecosim software (Ecopath with Ecosim is a mass balanced trophic model that accounts for fishing impacts on food webs), with one having trawlers fishing everywhere beginning at the turn of the century (year 2000) and the other with no trawling in the first 5 nautical miles off the Nigerian coast through the entire period of model simulation (1985–2004). Modeling results showed increases in catch for some fisheries during the study period. In addition, estimated biomass for some functional groups increased especially for Small Pelagic fishes along with Rays, Reef fishes, Large Pelagics, and shallow water shrimps. All other exploited species in our modeling scenarios were estimated to have declining biomasses. Our expectation that redistribution of fishing effort in NCW will increase negative impacts of fishing the nearshore ecosystem was not supported by model results. This counterintuitive result may be because fishing effort on average was mostly distributed in the deeper areas of the inshore waters. Although specie such as Reef fishes appear to benefit from closure of the first 5 NM to fishing, the benefits appear to be negligible. We present the first ecosystem model developed for NCW, and our research contributes to fisheries ecology by furthering understanding of tropical coastal food webs and ecological response to fishing, especially in highly perturbed ecosystems like NCW.