Accurate prediction of shear force distribution along the boundary in open channels is a key to the solution of numerous hydraulic problems. The problem becomes more complicated for meandering compound channels. A model is developed for predicting the percentage of shear force at the floodplain (%Sfp) of two-stage meandering channels using gene-expression programming (GEP) by considering five dimensionless parameters viz. the width ratio, relative depth, sinuosity, bed slope, and meander belt width ratio as the inputs in the model. Basing on the %Sfp, the apparent shear force along the division lines of separation in compound channels is selected for discharge calculation using the conventional channel division methods. An Enhanced Channel Division Method (ECDM) is introduced to calculate discharge by assuming interface line at main channel and floodplain junction. A modified variable-inclined (MVI) interface is suggested having zero apparent shear determined from flow contribution in the main channel and floodplain. The MVI interface is further used to calculate discharge in the meandering compound channels. Performance of the GEP model is tested against other analytical methods of calculating %Sfp. Error between the observed and calculated discharges using the MVI interface is found to be the minimum when compared to other interface methods. The enhance channel division method is successfully applied for validating the two available overbank discharge values for the river Baitarani at Anandapur (drainage area of 8570 sq. km), giving the minimum errors of 0.31% and 1.02% for flow depths of 7.5 m and 8.63 m, respectively. © 2020, Springer Nature B.V.