Flood pulse and biotic interrelationships control the food web dynamics of river floodplain systems. The Pantanal Plain in the Paraguay River Basin (Brazil) occupies 140,000 km2 of periodically flooded areas and is divided into 12 subregions with different characteristics related to the flood pulse duration, the vegetation, the type of soil, and the resources used in activities, particularly fishing. In this study, we used Ecopath with Ecosim (EwE) to model three oxbow lakes in the South Pantanal Plain, where there is no fishing activity, to test the similarity of the ecosystems, to identify the keystone species and the types of food web controls, and to determine whether these environments can support moderated fishing pressure. We found that the food webs of the oxbow lakes are similar to each other because, although they depend mainly on the presence or absence of predators, flood pulses similarly homogenize the lakes. The results highlight the importance of detritus in these food webs. In addition, the highest values of the keystoneness species index in the three models highlight the role of top predators (Hoplias malabaricus, Serrasalmus spp., Pseudoplatystoma reticulatum, birds, and mammals). Therefore, we suggest that the food webs in the three systems are subjected to an alternated control process: detritus controls the food web during the flood season and by the top predators during the dry season. The simulation outputs indicate that these oxbow lakes can sustain only moderate fishing because increasing the fishing pressure reduces the biodiversity and can negatively impact the top predators