First, you need to inspect the generator for the obvious.
• Did water enter the engine core or lubrication areas?
• Did water enter or submerge any electrical or electronics components?
After checking all of the above and determining that not water damage or penetration is present, I would simply start and run the generator for a short period of time. Shut down and check oil, and general.
Then restart and verify electrical output etc…
If you do have water penetration in the engine core – remove engine oil and flush the engine. Replace oil.
If electrical connections or components have been compromised, you may need to do cleanup or replacement as required.