Many of the Upper Missouri River dikes have been notched to create additional shallow water habitat (SWH, operationally defined as areas in the stream with depth < 1.5 m, and velocity < 0.75 m s−1) for fish populations. The goal of this study was to quantify the additional SWH gained from notching these dikes and to evaluate their performance under different flow conditions. A coupled field and numerical study was performed on a reach of the Missouri River, near Nebraska City, NE, which contains a number of dikes notched in 2004. The numerical simulations showed that the SWH criterion for depth was more difficult to satisfy in the study reach than the SWH criterion for velocity. Notching the dikes resulted in a slight shift of the bankline due to local erosion in the vicinity of the dikes and the formation of scour holes downstream of the notches. Results from the study suggested that notching the dikes had limited impact on the SWH because the area gained from the bankline shift was offset by the area lost from the scour holes formation. The performance of the notched dikes in sustaining the minimum habitat suitability conditions for the Missouri River ecosystem was also investigated. These conditions corresponded to discharges < 709 m3 s−1 for the period from mid-July to mid-August, or equivalently SWH areas > 5225 m2 dike−1 during the same period. Analysis of the Missouri River annual discharge records at the study site showed that the dikes can provide the minimum required SWH for mean annual discharges < 667 m3 s−1. For mean annual discharges > 667 m3 s−1, new alternative structures or restoration facilities were needed, in addition to the existing dikes, to sustain the minimum required SWH. The dikes were not effective in providing any SWH for mean annual discharges > 2000 m3 s−1. Copyright © 2010 John Wiley & Sons, Ltd.