Variability of sea surface temperatures (SST) in 1200–2000 CE is quite well-known, but the history of deep ocean temperatures is not. Forcing an ocean model with these SSTs, we simulate temperatures in the ocean interior. The circulation changes alter the amplitude and timing of deep ocean temperature fluctuations below 2 km depth, e.g. delaying the atmospheric signal by ~ 200 years in the deep Atlantic. Thus ocean circulation changes are shown to be as important as SST changes at these depths.