Field observations, laboratory experiments, and numerical modeling were used to better understand conditions producing suitable habitat for fish spawning, particularly lake trout, in the Great Lakes. The study focused on Shorehaven Reef, a natural reef near Barcelona in southwestern New York. Measurements of water velocities and levels were monitored during summer 2025 over multiple deployments using an acoustic Doppler current profiler situated at different locations on the reef. Laboratory experiments were conducted to demonstrate interactions between bottom shear stress and processes affecting fish egg settling into bottom substrate, and also to evaluate the effects of the reef on flow patterns. A nested numerical model was developed to study flow patterns in the area surrounding the reef. Results show increased shear stresses on the leeward side of the reef, which also is covered with relatively “clean” cobble (without silt) on which lake trout spawning has been documented. Artificial reefs need to be designed so that natural flow can maintain appropriate spawning habitat. Guidelines are presented for such design.