AbstractMixing processes in lakes are important in determining sedimentation zones and in setting the so‐called “wash zone”, the area of lake bottom in contact with an oscillating thermocline during wind‐driven internal seiche events. The wash zone also aligns with a sharp change in sediment roughness and hardness. Taken together, these rapid changes in temperature and sediment indicate that the wash zone is a distinctive ecotone in stratified lakes. Depth stratified randomised netting was used to develop count‐based habitat use models for three common benthic fish species as a function of depth or temperature covariates. Using data from two lakes with quite different wash zone depths, we show the wash zone to describe fish habitat for two of three benthic fish species by utilising the top 50% of estimated fish abundance as an indicator of habitat use. White sucker (Catostomus commersoni) habitat use was within the boundaries of the wash zone. Lake whitefish (Coregonus clupeaformis) habitat was adjacent and within the wash zone. Longnose sucker (C. catostomus) habitat use was in the deep areas of lakes dominated by sediment focusing and did not overlap white sucker. Lake whitefish habitat use overlapped both catostomids, but peak abundance of both lake whitefish and white sucker overlapped pointing to potential interactions between these species. Smaller lakes have less vigorous mixing processes and a narrower wash zone, so with a decline in lake size the likely area of the wash zone as habitat for benthic feeding fish would become smaller.