Grade-control structures (GCS) are commonly used to protect fish habitat by preventing excessive river-bed degradation in mountain streams. However, flow over the GCS can cause localized scour immediately downstream of the weir. This paper aims to develop more accurate models for prediction of the maximum scour depth downstream of GCS, using a more extensive dataset and evolutionary gene expression programming (GEP). Three GEP models are developed relating maximum scour depth and various control variables. The developed models had the lowest error compared to available models. A parametric analysis is performed for further verification of the developed GEP model. The results indicate that the proposed relations are simple and can more accurately predict the scour depth downstream GCS.