Reference estimates of seawater desalination costs for recent mega projects are all quoted in the range of US$0.50/m(3). This however does not reflect the recent trends of escalating fossil fuel costs. In order to analyze the effect of these trends, a recently updated version of the IAEA Desalination Economic Evaluation Program, DEEP-3, has been used to compare fossil and nuclear seawater desalination options, under varied fuel cost and interest rate scenarios. Results presented for a gas combined-cycle and a modular high-temperature gas-cooled reactor design, show clear cost advantages for the latter, for both Multi-Effect Distillation (MED) and Reverse Osmosis (RO). Water production cost estimates for the Brayton cycle nuclear option are hardly affected by fuel costs, while combined cycle seawater desalination costs show an increase of more than 40% when fuel costs are doubled. For all cases run, the nuclear desalination costs are lower and if the current trend in fossil fuel prices continues as predicted by pessimist scenarios and the carbon tax carried by greenhouse emissions is enforced in the future, the cost advantage for nuclear desalination will be even more pronounced. Increasing the interest rate from 5 to 8% has a smaller effect than fuel cost variations. It translates into a water cost increase in the range of 10-20%, with the nuclear option being the more sensitive.