Electrokineticmicroperistaltic pumps are important biomechanical devices that help in targeted drugging of sick body parts. This article is focused on mathematical modeling and analysis of some important aspect of such flows in a rectangular duct with wall properties. Effects of zeta potential, heat source, and deby length are also studied. Carbon nanotubes (CNTs) in the Newtonian base fluid are assumed as drugging material. A comparison of single‐walled CNTs and multiwalled CNTs is also presented. It is considered that the walls are flexible and encapsulating the region with limited permeability. The defined flow problem is modeled and analyzed analytically for the transport of CNT–water nanofluid. It is accepted that the flow is steady, nonturbulent, and propagating waves do have a considerably longer wavelength when compared to amplitude. The conditions and assumptions lead to a model of coupled partial differential equations of order two. The exact results using the eigenfunction expansion method are procured and shown accordingly. The predictions about the behavior of important parameters are displayed for single‐walled CNT and multiwalled CNT—water nanofluidic behavior—using figures. The impact of sundry parametersis are analyzed. The application of the current study involved a transporting/targeted drug delivery system using peristaltic micropumps and magnetic fields in pharmacological engineering.