During the previous century, the wetland area in the lower Missouri River alluvial valley was reduced by 39% because of river channelization and bank stabilization projects. The Great Flood of 1993 reversed the trend of wetland loss by creating 466 new wetlands in the alluvial valley between Kansas City and St. Louis, Missouri. We estimated amphibian occupancy, detection probability and number of species exhibiting evidence of reproduction in eight flood-created and 16 pre-flood existing wetlands from 1996 through 1998. We also evaluated whether hydroperiod (the number of days any water was present in a wetland from 20 February through 31 August) and distance to river predicted those values. Detection probabilities for adult amphibian species were relatively constant across years and ranged from 0.013 [Great Plains toad (Anaxyrus cognatus)] to 0.280 [Woodhouse's toad (Anaxyrus woodhousii woodhousii)]. Occupancy of adult amphibians differed across years and was not correlated with habitat features. Estimated occupancy probabilities for amphibian species ranged from 0.126 [Plains spadefoot (Spea bombifrons)] to 0.896 [boreal chorus frog (Pseudacris maculata)]. Almost double the number of amphibian species showed evidence of reproduction in existing wetlands (wetlands created before the Great Flood of 1993) when compared with that in flood-created wetlands. Similarly, temporary wetlands had nearly double the number of amphibian species showing evidence of reproduction when compared with permanent wetlands. Finally, the highest number of species showed evidence of reproduction in wetlands with spring–summer hydroperiods between 135 and 140 days. All these relationships suggest that the invasion and persistence of predators in wetlands negatively influence amphibian reproduction. If the Missouri River is allowed to reconnect with the alluvial valley, more predators may be introduced into wetlands, leading to reduced amphibian occupancy and reproduction. However, this connection will not likely occur over the entire alluvial valley and, therefore, should not adversely impact amphibians that find refuge in higher-elevation, non-connected regions of the alluvial valley. Copyright © 2011 John Wiley & Sons, Ltd.