The atmospheric and oceanic components of CLIMBER-3α are coupled via heat, freshwater and momentum fluxes.  The atmosphere-ocean fluxes are calculated separately for sea-ice and leads. Fluxes are exchanged with a time-step of half a day.
The coupler employs the same horizontal resolution as the ocean model (3.75° × 3.75°). The individual fluxes which contribute to the heat, freshwater or momentum fluxes are either calculated by the atmosphere or the ASI or in the coupler. In the first two cases, the fluxes are interpolated to the coupler's resolution; in the third case, the coupler makes use of the variables required from each module and interpolates these to its resolution to calculate the fluxes in its own grid.

Variables are interpolated bi-linearly, whereas for the fluxes a conservative interpolation scheme was employed in order to guarantee heat and mass conservation. The coupling procedure does not include any flux corrections for heat and freshwater fluxes, but for the momentum-flux the anomalies relative to the control run are computed and added to climatological data.

CLIMBER-3α includes CLIMBER-2's atmosphere-surface interface (ASI) (Petoukhov et al., 2000), which is based on the Biosphere-Atmosphere Transfer Scheme (BATS) (Dickinson et al., 1986). Each model grid box consists of one or several of six surface types: open water, sea ice, trees, grass, bare soil, and glaciers. For each type sub-, near- and surface characteristics, as well as surface fluxes, are calculated separately taking the different surface properties such as the albedo or roughness length into account.

Vegetation cover can either be prescribed or simulated as a function of climate through the VECODE terrestrial vegetation module (Brovkin et al., 1997), in turn affecting climate through characteristics such as the albedo, roughness-length and fraction of surface covered by snow.