The vertical distribution of the benthic fauna associated with soft sediments in sealochs was investigated by divers taking pairs of core samples at a series of depth levels along a transect from the shore out to a maximum depth of 25 m. Eight transects were worked, 5 in Loch Etive, 2 in Loch Creran and 1 in an adjacent area in Lochnell Bay outside the two lochs. The samples from each transect were objectively classified into hierarchical groupings by applying a clustering strategy to the values of an index of faunal similarity derived from the species abundances data. An attempt is made to relate the structures shown to physical differences measured along the transect in terms of depth, topography, sediment granulometry and exposure. In Loch Etive, the groupings were found to be best correlated with the pattern of intense vertical gradients in salinity and temperature. These are caused by the semi-permanent depression of surface salinity by terrestrial drainage. The faunal distributions showed best correlation with the degree of fluctuation of salinity, measured near the transect sites in a long-term hydrographic study, rather than with its mean value. This indicated that the range and speed of salinity fluctuations probably primarily control the observed pattern of vertical zonation of the typically estuarine and euryhaline marine species found in the samples. In Loch Creran and Lochnell Bay, the groupings may best be related to a complex of unstable conditions including wave exposure, sediment type and occasionally reduced surface salinity. Records currently considered sensitive have been removed from this dataset.