In the Oueme River, a lowland river in Benin, Africa, artificial ponds constructed in the floodplain (whedos) are colonized during the high-water period by a presumably random sample of fishes from the river channel. As water slowly recedes from the floodplain, fishes are isolated in whedos until they are harvested near the end of the dry season. I surveyed fishes in whedos and adjacent main-channel and floodplain habitats during two low-water (2008 and 2009) and one falling-water (2010-2011) periods, and measured a suite of physicochemical variables including dissolved oxygen, temperature, specific conductivity, and percent cover of aquatic vegetation in the falling-water period to investigate if fish assemblage structure of whedos resulted from stochastic or deterministic processes. I also investigated food web structure of whedos by analyzing carbon (delta13C) and nitrogen (delta15N) stable isotope ratios of fish and primary producer tissue samples, and samples of net primary production, soluble reactive phosphorus (SRP), NH4+, NO2-, and NO3- collected during the falling-water period. Whedos were covered with dense growth of aquatic vegetation, and dissolved oxygen concentrations were lower in whedos compared to a natural floodplain depression and the main channel. Multivariate analyses revealed that habitat types were distinct with regard to fish assemblage structure and abiotic conditions. Assemblages in whedos and natural floodplain depressions were differentiated from those of the river channel, with the floodplain habitats being dominated by piscivorous fishes that tolerate aquatic hypoxia. These results indicate that fish assemblage structure of whedos was influenced by deterministic processes during the falling- and low-water periods when these water bodies were isolated. Floodplain habitats were more nutrient-rich than the river channel, and whedos were net heterotrophic. Microphytobenthos and C3 macrophytes accounted for a large fraction of fish biomass in whedos, compared with the river channel, which was mainly supported by seston. Whedo food webs had fewer trophic transfers compared to the food web of the river channel.