Sounds like you washed muck into the alternator, it may dry out if you only got water in it, if oil/sludge it will need to be rebuilt/replaced.
More than tread lightly. Leave it like you were never there, nor anyone else.
'90 X-cab 4.88's 33 BFG AT's, rr ARB, Headers, Ignition upgrade, cold air induction.
'91 X-cab 5.29's 315's BFG MT's, rr ARB, custom bumper and flatbed