Some more information re your engine,(size, fuel injected, carbed, 2 stroke, 4 stroke, hours), fuel tank set up (built in or separate-above deck portable) would be a big help...

If the fuel is ethonol and has been sitting for awhile (without a stabilizer additive) it'll go bad in as quick as a month and also pick up moisture as well.

Your generic description could very well be a fuel issue. If carbed, the carbs should have a drain bolt at the bottom of each carb. I'd drain each one into a small (I use a clean tuna fish can) can and examine the fuel closely for water, crap in the fuel etc. A piece of crap in the carb can be getting sucked into the main jet closing it off as well. If you have a portable tank and the fuel is old, dump it and start with fresh..

If you have a large built in tank on an older boat, they do make a product to help get rid of the water without pulling the tank.

More information is really needed to go any further...