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Labyrinth weirs are a type of flow‐control structure often placed in rivers, canals, and at dams due to their ability to pass high discharges at relatively small heads. However, woody debris from the catchment may be transported by the river and collect against the structure and accumulate, become waterlogged and submerged, and negatively impact structure hydraulics and the adjacent river reach. In this study, field data from the labyrinth weir on the Brazos River (Texas, USA) and a laboratory study were used to evaluate the interaction between labyrinth weirs and submerged woody debris jams in river applications. Structure hydraulics, including discharge rating curves, were studied for five submerged woody debris jam scenarios. Debris volume, debris jam geometry, and debris influence on the flow field highly influenced discharge capacity of labyrinth weirs with an average reduction to the discharge coefficient of at least 11%, and a maximum reduction of 33%. This corresponded to an increase in upstream head ranging from 17 to 41% for the range of flows tested in the laboratory.