Accurate control and handling of fluids in microfluidic-based bio-medical devices is very important in diverse range of applications such as laboratory-on-chip (LOC), drug delivery, and bio-technology. Flow through medical devices such as kidney dialyzer and membrane oxygenator can be considered as laminar due to low Reynolds number and narrow channel geometry, thus requiring efficient utilization of passive modulation systems to improve fluid mixing in these devices. In the present work, numerical investigation of fluid flow and passive mixing effects is carried out for wavy-walled channel configurations. A two-dimensional computational model based on an immersed boundary finite volume method is developed to perform numerical simulation on a staggered Cartesian grid system. Further, pressure–velocity coupling of governing continuity and Navier–Stokes equations describing the fluid flow is done by SIMPLE algorithm. Fluid variables are described by Eulerian coordinates and solid boundary by Lagrangian coordinates. Linking of these coordinate variables is done using Dirac delta function. A momentum-forcing term is added to the Navier–Stokes equation in order to impose the no-slip boundary condition on the wavy wall. Parametric study is carried out to analyze the fluid flow characteristics by varying wave geometry factor (WG Factor) of crest–crest (CC Model) wavy wall configurations for Reynolds number ranging from 10 to 50. From this work, it is evident that incorporating wavy-walled passive modulators prove to be good and robust method for enhancing mixing in biomedical devices.