Sedimentation and clogging (colmation) of interstitial pore spaces with fine sediment particles is widely considered to be one of the most significant threats to lotic ecosystem functioning. This paper presents the results of a running water mesocosm study examining the effect of benthic and hyporheic fine sediment loading and particle size on the vertical movement and distribution of the freshwater amphipod Gammarus pulex. A gradient of fine sediment loading and different particle sizes were used to examine the ability of G. pulex from two body size classes to access and migrate vertically within subsurface sediments. We tested three hypotheses: (a) sediment loading would modify the distribution of G. pulex by limiting vertical movement; (b) the deposition of large particles and heterogenous sediments would limit the vertical movement of individuals more than homogeneous fine-grained sediments; and (c) large bodied individuals would be prevented from migrating vertically with increasing sediment loading and particle size/heterogeneity. Sediment loading, particle size and heterogeneity of deposited sediment had a significant effect on the vertical movement of individuals, with heterogeneous sand (0.125–4 mm) acting as the strongest barrier to the vertical movement of individuals through the infilling and clogging of interstitial spaces followed by coarse (1–4 mm) and fine sand (0.125–4 mm). Fine sediment loading and particle size acted as a filter on body size and limited the ability of large bodied individuals to migrate vertically to a greater extent than small bodied individuals. This study demonstrates that the effects of fine sediment on habitat availability and faunal movement is dependent on both sedimentological characteristics and an individual's body size. The results illustrate the importance of both abiotic and biotic factors when evaluating the ecological effects of fine sediment deposition.