from Present-Day Atmospheric Simulations Using GISS ModelE: Comparison to In Situ, Satellite, and Reanalysis Data
"The surface is split into four types: open water (including lakes and oceans), ice-covered water (again including lake ice and sea ice areas), ground (including bare soil and vegetated regions), and glaciers"
"k. Lakes
Over land there is a (currently fixed) lake fraction that can be variably ice covered. The lakes are represented with a two-layer energy and mass conserving scheme. The upper layer (minimum depth: 1 m) is assumed to be well mixed, and surface and underground runoff, precipitation, and downstream flow only interact with this layer. The second layer can be arbitrarily deep and exchanges heat, mass, and tracers with the upper layer through mixing driven by wind stirring and convection. "
" In deep lakes (that do not completely freeze up over winter), the lower lake temperature thus reaches a minimum of 4°C. Ice-covered lakes are allowed to completely freeze over (i.e., there is no minimum lead fraction)."
"l. Sea and lake ice
Sea and lake ice processes are considered together, although obviously there are some differences [specifically, lake ice is fresh, not advected, and the turbulent heat and mass flux at the base of the ice is more simply parameterized than for (saline) sea ice]"
It is unclear if the lakes are in the land model or ocean model. Ocean SSTs are missing over Great Lakes, but in the paper referenced above, Fig 21 shows lake ice on/off dates and Great Lakes are omitted; also, ocean wind fields in Fig 20 show values over the Great Lakes.