Flow and transport studies in fractured aquifers have been widely carried out by adopting the parallel plate approximation for fracture walls. However, the fractures existing in the field scenario may not always possess parallel walls and may have spatially varying fracture widths. Hence, the parallel plate conceptualization of a real fracture may be highly idealistic in some cases. The principal aim of this work is to numerically investigate the coupled dissolution and transport of benzene along a sinusoidal fracture under non-uniform flow conditions, and to compare the simulation results with the results obtained using the parallel fracture model. Results from the simulation study indicate that the parallel plate approximation of a sinusoidal fracture may lead to incorrect prediction of dissolved benzene concentration along the fracture. A sensitivity analysis is carried out to investigate the sensitivity of sinusoidal fracture parameters, such as amplitude, wavelength and average fracture aperture on the dissolution and transport of benzene within the fracture. Simulation results obtained using the parallel plate idealization of sinusoidal fractures with high amplitudes and low wavelength is found to deviate more from the real field scenario. Sensitivity of the inlet fracture pressure on concentration distribution of benzene is also analyzed. Transport of dissolved benzene is found to be significantly sensitive to fluid pressure at the fracture inlet. © 2017, Springer International Publishing AG.