My Alpha One overheats, got stuck in some mud how do I clean the intake?

while out on the Intracoastal the other day, i anchored my boat and she drifted in to very shallow water. when i started her i know i kicked up alot of muck,,,, about 15 minutes later my left engine made a funky clanking sound, then shut down when i looked the Temp gauge was over 200 and white smoke from the cooling system was coming out... I let her set for about an hour and limped her back to my marina on the other engine, which ran great... could I have clogged the ocean water intake and if so how do i clean it.