It won't necessarily be related to driving in the wet.
Water in the fuel would make it hard to start and run. Water in the oil, however, isn't that good and can cause damage but unless there is a leak somewhere in the crankcase (eg if the governor hole at the top of the block isn't sealed with either a banjo bolt for fuel pump vacuum or a bolt).
Knocking can be a number of things including a con-rod that has picked up on either end (but most commonly the bottom) or excessive crank end float.
Check the latter first by simply pulling and pushing the crank long its axis. A little play is ok. The former requires a look at the bearings but is simple - drain the oil, remove the side casing and undo the cap of the conrod. The bearing should be smooth and of uniform colour.
Graeme
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