Subsurface sediments offer an important refuge that support the survival and persistence of river invertebrates during adverse surface conditions. Access to refuges for invertebrates varies with differing hydrological and substrate characteristics, especially the proportion of fine sediment. This study examines whether substrate characteristics influence the use of the hyporheic zone as an invertebrate refuge during a fine sediment disturbance event. We used 12 outdoor stream mesocosms to examine the vertical migration of benthic and hyporheic invertebrates to fine sediment loading. Each mesocosm was filled with coarse or experimentally colmated sediments. After 69 days, a fine sediment pulse of three varying fine sediment concentrations was added to the stream mesocosms. Both before and after the fine sediment pulse, a distinct gradient in the abundance and richness of hyporheic invertebrates was apparent with depth. Hyporheic abundance and taxonomic richness decreased at 5 cm and increased at 18 cm during fine sediment loading, indicating vertical migration of invertebrates from the benthic to hyporheic zone. Our study provides support for the hyporheic zone as a refuge for benthic invertebrates during fine sediment disturbance events. We also found evidence that movement pathways within subsurface sediments were still accessible and permitted bidirectional migration of individuals between the benthic and hyporheic zone in the coarse and colmated sediments during fine sediment loading. Understanding how increased fine sediment deposition affects streambed porosity will be increasingly important with ongoing climate change and anthropogenic sedimentation.