More than 400 km of high-resolution seismic and magnetic data were collected over central Lake Ontario to investigate a possible lakeward continuation of the Clarendon-Linden fault structure of western New York State. The seismic data show that a bathymetric lineament that crosses the lake along the projected strike of the fault is a west-facing partly buried bedrock ridge, here called the Scotch Bonnet Rise. Its 30-m relief is similar in magnitude and orientation to observed offsets on the north-striking Clarendon-Linden fault. Magnetic data from the lake and earlier magnetic and gravity data collected in western New York show that the Scotch Bonnet Rise and the Clarendon-Linden structure coincide with the east flank of a linear magnetic trough and the west flank of a series of circular Bouguer gravity highs. The source of these geophysical anomalies is clearly in the Precambrian basement, suggesting that the observed deformation in the Paleozoic section is superimposed on a pre-existing Precambrian structure. Although the unconsolidated lake sediments show no evidence for Holocene movement of the fault, the geophysical evidence indicates that the Scotch Bonnet Rise is a continuation of the Clarendon-Linden structure and that together they form a linear feature more than 150 km long.