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Secondary circulation is known to be an important feature of many atmospheric and laboratory boundary layers. The presence of streamwise, helical, counterrotating vortices is documented here for the first time in the bottom boundary layer of a large natural body of water. Simultaneous vertical profiles of velocity and temperature were recorded on either side of a sedimentary furrow on the floor of Lake Superior (depth = 100 m) in November 1985. Flow roughness length zo was estimated to be 0.3 cm. Friction velocity u* and turbulent boundary layer thickness LW were estimated for each profile allowing for stratification effects. Typically, LW ≈ 10 m. Thermal stratification near the lake bed was an important constraint to boundary layer development; bottom mixed layers were absent in most cases. Mean flow toward the furrow at lower levels within the boundary layer (z/LW<0.37) and mean flow away from the furrow at higher levels (0.37 < z/LW < 1.65) were observed for near‐bottom speeds greater than 6 cm/s when mean flow direction was within 25° of the furrow direction. This implies helical vortex pair circulations with upward motion over the furrow, consistent with earlier hypotheses. Cross‐stream (secondary) flows were typically 5% of the free stream (primary flow) speed. Streamwise vorticity in the range 1.5 m ≤ z ≤ 5 m was estimated to be 2.1×10−3 s−1.