The highly energetic geological processes inevitably accompanying the Genesis Flood must have generated an enormous heat load without raising environmental temperatures beyond biological endurance limits. This is the second in a series of papers intended to identify and, where possible, to quantify the key sources of Flood heat. Our concern here is with the thermal history of the oceans viewed as a boundary condition on models of the Flood and post-Flood periods. Having reviewed palaeothermometry based on the oxygen-18 content of marine fossil shells (δ18O) in the first paper, we review here the development and application of alternative palaeothermometers. These include: (1) the magnesium/calcium (Mg/Ca) ratio in calcite fossil shells, notably those produced by foraminifera; (2) the strontium/calcium (Sr/Ca) ratio in scleractinian (aragonitic) corals; (3) biomolecular indicators including the alkenone unsaturation index, the iDGDT index (or TEX86) and the long diol index (LDI); (4) the clumped isotope (Δ47) index, which relates to the temperature-sensitive proportion of the joint heavy-isotope bond 13C-18O in carbonate-containing molecules in fossil materials. All these methods and the results they produce are subject to significant complications and uncertainties. However all constitute active, developing fields of research, especially the clumped isotope index, and many studies combine two or more of these methods. This provides additional information (e.g. salinity and continental ice volume) and facilitates assessment of complicating factors. In Mg/Ca palaeothermometry, the most mature of these methods, an uncertainty of ± 2.5ºC (sometimes less) can reasonably be claimed provided that complicating factors have been assessed and accounted for. The most important conclusion from this review, based on analysis of combined δ18O-Mg/Ca data and sea level records, is that deep ocean water has cooled by 12ºC since the early Eocene. This supports the conclusion in the first paper that deep ocean temperatures never exceeded 13ºC through the Cenozoic, an important constraint on Flood and post-Flood models. Further constraints on such models are provided by ocean temperatures reconstructed from studies focused on particular areas and particular points in the geological record. We have also identified several time-related puzzles and anomalies in the conventional literature which deserve investigation from a creation science perspective.