Lake trout reproduce widely in Lake Superior but little in Lake Huron. We examined whether survival of lake trout eggs and fry in either lake was reduced by physical disturbances and swim-up mortality. Eggs were collected from feral lake trout in Lake Superior and placed in 108 plastic incubators. A total of 48 incubators was set at Partridge Island Reef in southern Lake Superior, 48 were set at Port Austin Reef in southern Lake Huron, and 12 were held as controls inflowing well water at a laboratory. Survival-to-hatching of these eggs at Partridge Island Reef (18%) was significantly different from that at Port Austin Reef (43%) and significantly different in the laboratory (88%) from that at either reef (P < 0.05). During egg-fry incubation from 28 October 1987 to 5 May 1988, 11–18 cm of sediment accumulated in sediment traps placed on the reefs but < 1 cm of sediment was present on each reef in May 1988. Analysis showed that 44% of the eggs at Port Austin Reef and 28% of those at Partridge Island Reef were buried and killed by sediments. During the first week after deployment, mean wave energy was 90% higher at Partridge Island Reef and significantly different from that at Port Austin Reef. Wave energy may be a habitat condition that makes Partridge Island Reef less suitable than Port Austin Reef for incubation of lake trout eggs. Fry from eggs incubated at all three sites experienced no swim-up mortality. We conclude that in 1987–88 habitat conditions required for survival of lake trout eggs were more suitable at Port Austin Reef than at Partridge Island Reef.