Rust spots on water heater -- time to replace?
Most water heaters have an inner tank surrounded by an insulation material surrounded by the outer shell.  If it is the outer shell that has some rust spots then there probably is not anything to be worried about.  So depending on where the rust spots are located you may not need to worry about them at all.

But considering that you are seeing rust spots on your water heater that might mean that it is fairly old.  If it is old, then you should think about replacing your water heater... a new water heater will save you a lot of money in energy costs (new ones are much more energy efficient).