Flow resistance is often one of the most important subjects required for hydraulic computations and designs. The existing methods to estimate the resistance coefficients have been developed for uniform flow and small grain size streams. Using the methods for non-uniform flow conditions can be led to considerable error in the determination of resistance to flow. This research investigates flow resistance in channels with cobble on bed and vegetation on sides. Accordingly, geometric and hydraulic characteristics of non-uniform flow and intermediate roughness scale were measured in two case of with and without plant. For the first case; three reaches were selected in around of Khansar. For the second case; two reaches were selected: one reach sited in old channels and the other reach from Marbore River in Koohrang. Validation of the logarithmic and the parabolic velocity distribution laws has investigated using measured velocity profiles in this study. Results showed that, the logarithmic law is valid for the entire reaches however the parabolic law isn’t valid for reaches with plant on sides. In addition, shear velocity which is a vital factor in predicting flow resistance, was calculated from three methods: the logarithmic, the boundary-layer characteristics and the simplified St- Venant equation. Comparison of these methods showed that the logarithmic method estimation was sensitive to determination of reference level. Also St-Venant equation is very sensitive to determination of bed and friction slopes. Therefore the both methods aren’t recommended for this study. Finally, the boundary-layer characteristics method is suggested for estimation of shear velocity in coarse-bed channels with vegetation on sides. In reaches which were without plant, using nonlinear regression through SAS software, a formula was developed for estimation of flow resistance in intermediate roughness scales. In this formula; aspect ratio, roughness ratio and parameter of particle incipient motion have significant influence on flow resistance prediction. But assessment of reaches with plant on sides showed that available parameters aren’t adequate for realization of flow resistance. This case request further investigations to improve our understanding from interaction of plant and cobble on flow resistance.