Erosion, transport, and deposition of a river-bed has attracted attentions from various disciplines. To understand those issues, bed shear stress should be evaluated first. However, calculating bed shear stress with existing formulas have certain limitations because uniform and/or gradually-varied flow was assumed in their studies, which is hardly found in an actual river. Therefore, direct applying them into three-dimensional complex flow field, such as flow around a bridge obstruction or a large-rock, is questionable. Thus, laboratory experiment was conducted in a flume and the results were used to suggest a method of bed shear stress estimation in the complex flow field. To generate the complex flow field, three different width of obstruction was constructed and installed in one side of the flume. Water depth, velocities, and turbulence intensities were measured, and the measurements were used as input variables of four different widely used existing shear stress formulas for their evaluation. Then, the effects of local turbulence on the shear stress were discussed in terms of Reynolds stress and turbulent kinetic energy (TKE) measured under a wide range of flow variables. Based on the findings, bed shear stress can be estimated with an empirical correction factor for the local turbulence around the obstruction where elevated region of bed shear stress is found, and the experimental result shows that the correction factor is function of the value of flow contraction ratio. The results are expected to be a useful outcome to understand the mechanism of geomorphological change under rapidly-varied non-uniform flow.