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Transport and migration of elongated, deformable micrometer-sized particles around circular obstacles is investigated. This study is specifically motivated by the need to understand the movement and environmental impact of microplastic fibers (microfibers), particularly as contaminants in groundwater resources. Through microscale modeling, we examine how deformation, motion, and localization of microfibers are affected by medium morphology and local flow inhomogeneities. Extensive numerical simulations are performed to study the complex fluid–solid interactions taking place and to reveal the connection between microfiber transport dynamics and the arrangement of periodic and random obstacles. The trajectories of microfibers, as well as hotspots of their accumulation within both periodic and random structured media, are studied. We show that a random structured medium gives rise to anomalous transport features, such as breakthrough long tailing. A generalized probabilistic framework based on continuous time random walk is utilized to describe the upscaled transport model and capture the memory effects as well as the non-Fickian transport features. The upscaled model parameters, including effective velocity, dispersion coefficients, and transition time distributions, are extracted from direct numerical simulations.