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Over the course of a year, we conducted three field deployments in South San Francisco Bay to examine seasonal variability in bottom drag. Our data consisted of turbulence measurements both within and outside the bottom boundary layer, and benthic characterization surveys adjacent to our study site. Our results suggest that canopies of benthic worm and amphipod feeding tubes, which were denser during the summer, can increase the drag coefficient by up to a factor of three relative to the smoother beds found in the winter and spring. The extent of the drag increase varied depending on the measurement device, with the greatest increase inferred by measurements taken further from the bed. The small scale and temporally‐varying population densities of these living roughness elements pose significant challenges for hydrodynamic models, and future work is needed to begin incorporating benthic biology statistics into drag coefficient parameterizations.