The sedimentary sequence preserved in the isolation basin at Loch nan Corr (NW Scotland) represents a high resolution record of environmental changes over the last 9.5 ka (virtually the entire Holocene). The final isolation of the basin from the sea is recorded over a 6 m sediment sequence lasting c. 7000 years as the rock sill of the basin passes through the intertidal zone. This isolation is due to relative sea-level fall associated with isostatic rebound from the melting of the Last Glacial Maximum ice sheet. Combining faunal counts of foraminifera and thecamoebians from the same sample preparations allows an accurate reconstruction of sea-level and environmental changes at this site over the Holocene. This study shows the potential for isolation basins in mesotidal areas to provide a series of sea-level index points from a single isolation contact thus improving the ease and accuracy of sea-level reconstructions. Biostratigraphic data improve our understanding of the ecology of foraminifera in these relatively unstudied rock-enclosed lagoonal ecosystems. It seems likely that Miliammina fusca can tolerate the generally low and highly variable salinities in these lagoonal settings more readily than any other foraminiferal species.