The Mackenzie Trough provides a high resolution signal for paleoceanography as a result of high sedimentation rates at the mouth of the Mackenzie River. Three cores were collected along a transect covering a depth range of 58–671 m and the time period of the last 11 500 cal BP. Prior to the last ∼10 000 cal BP, the distal core is characterized by laminated sediment and a foraminiferal fauna of Arctic Bottom Water calcareous species and abundant planktic foraminifera suggesting little freshwater runoff and (or) perennial sea-ice cover. This occurs at a similar time as laminated sediments from the west of this site, which have been suggested to be part of the Lake Agassiz flood outburst and (or) cold period. If this outburst occurred, the very positive oxygen isotope values from our core (PC3; >+3.0 ppm) indicate that it did not flow through the Mackenzie Trough. After 9000 cal BP, the faunas in the three cores differ because of timing and different water depths. However, it is possible to see a progression of cold saline water prior to 10 000 cal BP, with a freshening of surface water after 10 000 cal BP where tintinnids (brackish water ciliates) occur with incursions of deep water Arctic calcareous species to ∼3000 years BP. A sequence of mixed faunas appears as sea ice returns, at least periodically in the last 3000 cal BP; but (in core PC2 only) a return to more sea ice is recorded by both foraminifera and dinocysts in the last few hundred years.