Rocks above and below the Precambrian-Palaeozoic unconformity at the base of many Palaeozoic sedimentary basins of mid-continental North America are distinguished by secondary K-feldspar, chlorite and illite. Thrusting of the Appalachian foreland is generally considered responsible for the fluid migrations which caused this alteration. We have examined secondary chlorite and illite from Cambro-Ordovician rocks which overlie the unconformity in southern Ontario, Canada. This area is situated along the interface between the Michigan and Appalachian basins. Water involved in chloritic alteration at ~150°C has an O isotope composition compatible with a basinal brine evolved from seawater. Brine migration was probably triggered by the Taconic Orogeny to the east. In comparison, the secondary illite (365–321 Ma) largely postdates the Acadian Orogeny, and the illite-forming fluids have stable isotopic compositions typical of tepid (~40–55°C) meteoric water. We suggest that basement arches beneath southern Ontario were reactivated by this orogeny, which facilitated introduction of meteoric water. Similar alteration in underlying Precambrian rocks shows that fluid flow was focused along the unconformity during the regional Ordovician brine migration, as well as during the localized Mississippian introduction of fresh water.