<p>The motivation of this study stems from the need to accurately model blood flow in stenosed arteries where surface roughness and ion-slip effects significantly alter hemodynamics. Understanding these mechanisms is essential for developing improved diagnostic approaches and biomedical devices for cardiovascular treatment. The present work aims to analyze the peristaltic transport of Williamson nanofluid in a rough, porous, and magnetized arterial environment with the inclusion of Joule heating, viscous dissipation, nonlinear thermal radiation, Brownian motion, thermophoresis, activation energy, and motile microorganisms. A mathematical model is formulated with governing equations and realistic boundary conditions, and approximate analytical solutions are obtained using the homotopy perturbation method. The findings exhibit that as the wall roughness amplitude ratio and wall roughness pitch ratio increase, the critical velocity declines, while electromagnetic and thermal parameters strongly affect flow, temperature, and concentration distributions. The novelty lies in the surface equation being defined as a function of both spatial coordinates and time simultaneously, which enhances our ability to capture dynamic variations in blood flow. This development contributes to better prediction of hemodynamics in arteries affected by atherosclerotic plaques and provides valuable insights for biomedical applications in diagnosis and treatment.</p>