The evolution of the potential vorticity (PV) in the deep waters is diagnosed from output of the Hadley Centre Climate Model over a 1000 year integration. Extensive regions of low PV are formed whenever there is an inflow of dense fluid across the equator into a relatively isolated basin. Initially, the model reveals low contrasts in PV in the deep waters over the North Pacific and higher contrasts over the Southern Hemisphere and North Atlantic, which are consistent with climatological diagnostics. However, a drift in the climate model leads to the northward influx of bottom water weakening in the Pacific but strengthening in the Atlantic. This change in overturning circulation leads to the PV along deep neutral surfaces acquiring a weaker contrast over the North Atlantic compared with the Southern Hemisphere and the North Pacific. Transient tracer experiments suggest that these regions of low PV are useful in identifying abyssal layers that are strongly ventilated from across the equator.