Plastic microfibers are among the most abundant microplastic pollutants in wastewater systems, where their aggregation strongly influences transport, retention, and removal efficiency. Predictive modelling of microfiber agglomeration is therefore essential for designing effective separation strategies and supporting sustainable wastewater management within a circular-economy framework. This study introduces a multiscale, particle-based modelling approach to investigate the dynamics and aggregation of deformable plastic microfibers in shear flow. The methodology is based on smoothed particle hydrodynamics (SPH), enabling fully resolved fluid–structure interactions and hydrodynamic coupling between flexible, slender microfibers. Fibers are represented as deformable bodies whose bending, alignment, and interactions evolve dynamically with the surrounding flow field. Simulation results demonstrate that slender microfibers exhibit a strong propensity to aggregate even in simple shear flows, driven by deformation-induced alignment and near-field hydrodynamic interactions. The proposed framework provides a mechanistic basis for understanding microfiber aggregation and offers a predictive tool for optimising microplastic capture and treatment processes.