The traditional view of the geomorphic evolution of the southern Canadian Atlantic margin is one of gradual exhumation and peneplanation following Triassic–Jurassic rifting. Thermal modelling of apatite fission track data from pre-Carboniferous granitic basement in Nova Scotia and from Permian and Triassic sandstones from Nova Scotia, New Brunswick, and Prince Edward Island suggest a more complex thermal evolution of the onshore part of the margin. Models clearly indicate significantly elevated regional paleotemperatures during Jurassic time, and as much as 30 °C of post-Paleocene cooling. Model-predicted paleogeothermal gradients for granitic samples from the Digby D-1 well are normal, ranging from 15 to 20 °C/km. Post-Paleocene cooling may be attributable to the combined effects of 13 °C of exhumational cooling from erosion of approximately 700 m of post-Aptian sediments caused by decreased eustatic sea levels, and 8–17°C of cooling from the propagation to depth of a 10–20 °C decrease in paleo-mean annual surface temperatures between Late Cretaceous time and the present. The combined effects of burial heating related to increased eustatic sea level and the propagation to depth of higher paleo-mean annual surface temperatures in the Late Cretaceous may also explain elevated vitrinite reflectance levels in Cretaceous lignites and in Jurassic strata in the Fundy Basin of Nova Scotia. These models demonstrate that the traditional view of passive peneplanation and slow exhumation of the margin since Early Jurassic time is not tenable.