Abstract The existence of lentic larval lamprey populations has been recognized since the late 1950s. Yet little formal research has been conducted on their depth distribution and the determinants of habitat selection. A calibrated electrosampter mounted on the submersible Johnson Sea-Link II was used in 1985 to quantitatively sample more than 1,200 m 2 of varying substrate in Batchawana Bay, Lake Superior, in tandem with a mark/recapture program. Of 5,269 marked ammocetes released at depths greater than 22 m and 1,300 released at depths less than 10 m, none was recovered with the submersible near specific release points. However, 16 deep released individuals and 113 shallow released individuals were recovered during routine Bayer 73 treatments up to 3.5 km from initial release points. A cross-factor study to test the relative importance on habitat selection of substrate particle size distribution versus thermal acclimation below the thermocline was conducted in 1986. Neither substrate particle size distribution nor thermal acclimation seem to explain the general absence of ammocetes at depths greater than 15 m. Gross lentic habitat selection may revolve around the nearshore distribution of food particles and the interdiction of the thermocline along the leading face of alluvial fans in Batchawana Bay.