There is large uncertainty in the future sea level change at regional scales under anthropogenic global warming. This study uses a novel design of ocean-only general circulation model (OGCM) experiments to investigate the ocean’s response to surface buoyancy and momentum flux perturbations, as part of the Flux-Anomaly-Forced Model Intercomparison Project (FAFMIP), and compares with results from coupled, atmosphere-ocean GCM (AOGCM) experiments. Much of the inter-model spread is driven by the response to surface heat flux perturbations. In a multi-model ensemble of OGCMs forced with identical surface heat flux perturbations, regional sea level and ocean heat content changes demonstrate considerable disagreement, especially in the North Atlantic. Spread in both residual mean advection and diapycnal diffusion changes contribute to much of the multi-model disagreement over regional heat content change. Residual mean advection changes are related to the large spread in simulated Atlantic meridional overturning circulation (AMOC) weakening (20-50%). We find approximately 10% more AMOC weakening in response to surface heat flux perturbations in AOGCMs relative to OGCMs with consistent ocean models. This enhanced AMOC weakening is driven by an atmosphere-ocean feedback which amplifies the surface heat flux perturbation. In the North Pacific, there is little agreement amongst the ensemble over which processes lead to ocean warming, with varying contributions from residual mean advection and diapycnal diffusion. For the Pacific basin, the atmosphere-ocean feedback reduces sea surface temperature (SST) warming by 0.5°C. In the Southern Ocean, the atmosphere-ocean feedback is not generally important for buoyancy and momentum flux perturbations.