Zooplankton in the ocean respond to visual and hydro-mechanical cues such as small-scale shear in turbulent flow. In addition, they form strong aggregations where currents intersect sloping bottoms. Strong and predictable tidal currents over a sill in Knight Inlet, Canada, make it an ideal location to investigate biological behaviour in turbulent cross-isobath flow. We examine acoustic data (38, 120 and 200 kHz) collected there during the daylight hours, when the dominant zooplankters, Euphausia pacifica have descended into low light levels at ∼90 m. As expected, these data reveal strong aggregations at the sill. However, they occur consistently 10-20 m below the preferred light depth of the animals. We have constructed a simple model of the flow to investigate this phenomenon. Tracks of individual animals are traced in the flow and a variety of zooplankton behaviours tested. Our results indicate that the euphausiids must actively swim downward when they encounter the bottom boundary layer (bbl) to reproduce the observed downward shift in aggregation patterns. We suggest that this behaviour is cued by the small-scale shear in the bbl. Furthermore, this behaviour is likely to enhance aggregations found in strong flows at sills and on continental shelves.