In rivers, small and lightweight microplastics are transported downstream, but they are also found frequently in riverbed sediment, demonstrating long-term retention. To better understand microplastic dynamics in global rivers from headwaters to mainstems, we developed a model that includes hyporheic exchange processes, i.e., transport between surface water and riverbed sediment, where microplastic retention is facilitated. Our simulations indicate that the longest microplastic residence times occur in headwaters, the most abundant stream classification. In headwaters, residence times averaged 5 hours/km but increased to 7 years/km during low-flow conditions. Long-term accumulation for all stream classifications averaged ~5% of microplastic inputs per river kilometer. Our estimates isolated the impact of hyporheic exchange processes, which are known to influence dynamics of naturally occurring particles in streams, but rarely applied to microplastics. The identified mechanisms and time scales for small and lightweight microplastic accumulation in riverbed sediment reveal that these often-unaccounted components are likely a pollution legacy that is crucial to include in global assessments.