Reefs are used for spawning by Great Lakes fishes such as the lake trout Salvelinus namaycush, lake whitefish Coregonus clupeaformis, and cisco C. artedi. We designed egg funnels as a new type of sampling gear for quantifying egg deposition while minimizing losses of eggs to physical disturbance and predation. Egg funnels were compared with traditionally used egg bags to quantify egg deposition by spawning fish. In addition, the efficiencies of the egg funnels and egg bags were measured by seeding each gear type with artificial lake trout and lake whitefish eggs in situ. Egg funnels were as efficient as or more efficient than egg bags for capturing artificial eggs and naturally deposited lake trout eggs in both 2008 and 2009. Egg funnels had lower efficiency than egg bags for capture of natural coregonid eggs in 2008, potentially due to avoidance of the gear by spawners; gear avoidance was reduced by burying the egg funnels more deeply in 2009. Accurate estimates of egg deposition will assist fisheries managers in making more-informed decisions for management actions, such as stocking strategies and habitat protection.