The height of a guyot as measured from the surrounding regional sea floor to the volcano's slope break records the water depth at the time the guyot submerged. Thus guyot heights may be used as indicators of the paleodepth of the surrounding ocean floor. We compile data on the heights of 68 intraplate guyots and atolls in the Pacific Ocean as well as 46 volcanic islands in the Pacific, Atlantic, and Indian Oceans. We find that guyot heights generally increase with the age of the lithosphere upon which they were emplaced, although there is a large amount of scatter. In nearly all cases, seamount height, and thus seafloor paleodepth, is less than expected of normal seafloor. These results suggest that most of the volcanoes in this study formed on anomalously shallow seafloor, consistent with formation at hotspots. To characterize thermal anomalies associated with these hotspot swells, we model guyot heights by calculating the isostatic uplift predicted for normal lithosphere that has been partly reheated and is underlain by anomalously hot mantle. This model is able to explain the anomalous water depth at most of the seamounts with hotspot thermal anomalies of 100°–300°C. The heights of a few volcanic chains, however, are not anomalously low, suggesting that these volcanoes are not associated with hotspots. In addition, the observed trend of Hawaiian‐Emperor guyot heights as well as the subdued morphology and gravity signature of the oldest Emperor seamounts supports our hypothesis that Cretaceous age Meiji seamount may have formed on or near a spreading center.