The continental shelf west of Scotland has a veneer of medium to coarse sands and bioclastic gravels resting on basement, but in enclosed depressions (called deeps) the sediments are muddy. Sediment cores from two deeps have been studied: Muck Deep (170 and 218 m) and Stanton Deep (167 m). The live and dead foraminiferal assemblages from these shelf deeps differ in several ways. The live forms are mainly free-living taxa concentrated in the surface 0.0 to 0.5 or 1.0 cm sediment layer. The standing crop has a positive correlation with % Total organic carbon (TOC) and wt. % sediment <63 μm but a negative correlation with estimated organic carbon flux. The correlation coefficient between dominant living species and measured environmental parameters varies in magnitude and sign according to whether standing crop or relative abundance data are used, showing the need for caution in interpreting such relationships. The dead assemblages comprise a mixture of around 50% in situ forms derived from the live assemblages plus around 50% of allochthonous taxa (without living representatives), mainly having an attached or clinging mode of life, and considered to be transported in from the surrounding shallower, higher energy shelf. The transported forms are mainly <250 μm in size and probably travelled as suspended load. The abundance of dead tests is high (maximum around 12,000 and 52,000 cm−3 for Muck and Stanton deeps, respectively) and show a logarithmic increase with increasing proportion of the 63–125 μm sediment fraction. These observations confirm that the shelf deeps form depositional sinks for finer terrigenous and biogenic material. This study demonstrates the complexity of assemblage formation in low energy depressions on a moderate to high energy continental shelf. It also demonstrates the importance of determining the in situ and transported components in order to make a reliable environmental interpretation of the preserved assemblages. The high abundance of dead tests indicates very slow accumulation rates which are typical of a maximum flooding surface starved of detrital sediment.