The short answer is yes, but salt water is much harder on your boat than fresh water.

After running in salt water, it's a good idea to:

Rinse the entire boat with fresh water.
Flush the cooling system with fresh water if your boat uses water cooling.
Dry everything thoroughly before storing it.
Spray metal parts and bearings with a corrosion inhibitor to help prevent rust.
Check the flex shaft and grease it regularly.

Fresh water is generally much easier on electronics, bearings, and hardware, so it requires less maintenance.

For those of you who run in the ocean, what else do you do after each outing? Any tips for preventing corrosion or making your boats last longer?