Two coupled climate models, differing primarily in horizontal resolution and treatment of mesoscale eddies, were used to assess the impact of perturbations in wind stress and Antarctic ice sheet (AIS) melting on the Southern Ocean meridional overturning circulation (SO MOC), which plays an important role in global climate regulation. The largest impact is found in the SO MOC lower limb, associated with the formation of Antarctic Bottom Water (AABW), which in both models is enhanced by wind and weakened by AIS meltwater perturbations. Even though both models under the AIS melting perturbation show similar AABW transport reductions of 4–5 Sv (50%–60%), the volume deflation of AABW south of 30°S is four times greater in the higher resolution simulation (−20 vs. −5 Sv). Water mass transformation (WMT) analysis reveals that surface-forced dense water formation on the Antarctic shelf is absent in the higher resolution and reduced by half in the lower resolution model in response to the increased AIS melting. However, the decline of the AABW volume (and its inter-model difference) far exceeds the surface-forced WMT changes alone, which indicates that the divergent model responses arise from interactions between changes in surface forcing and interior mixing processes. This model divergence demonstrates an important source of uncertainty in climate modeling, and indicates that accurate shelf processes together with scenarios accounting for AIS melting are necessary for robust projections of the deep ocean's response to anthropogenic forcing.