In northern Fennoscandia, semi-alluvial boulder-bed channels with coarse glacial legacy sediment are abundant, and due to widespread anthropogenic manipulation during timber-floating, unimpacted reference reaches are rare. The landscape context of these semi-alluvial rapids—with numerous mainstem lakes that buffer high flows and sediment connectivity in addition to a regional low sediment yield—contribute to low amounts of fine sediment and incompetent flows to transport boulders. To determine the morphodynamics of semi-alluvial rapids and potential self-organization of sediment with multiple high flows, a flume experiment was designed and carried out to mimic conditions in semi-alluvial rapids in northern Fennoscandia. Two slope setups (2% and 5%) were used to model a range of flows (Q1 (summer high flow), Q2, Q10, and Q50) in a 8 × 1.1 m flume with a sediment distribution analogous to field conditions; bed topography was measured using structure-from-motion photogrammetry after each flow to obtain DEMs. No classic steep coarse-bed channel bedforms (e.g., step-pools) developed. However, similarly to boulder-bed channels with low relative submergence, at Q10 and Q50 flows, sediment deposited upstream of boulders and scoured downstream. Because the Q50 flow was not able to rework the channel by disrupting grain-interlocking from preceding lower flows, transporting boulders, or forming channel-spanning boulders, the channel-forming discharge is larger than the Q50. These results have implications for restoration of gravel spawning beds in northern Fennoscandia and highlight the importance of large grains in understanding channel morphodynamics.