If the water was very deep or your hubby drove through it fast, some water may have made it past the air filter and was sucked into the engine.
Unlike air, water does not compress. If one cylinder sucked in more than approx. 50 cc or so of water, the piston, valve(s) or connector rod may have become damaged by trying to compress the uncompressable. This would stall the engine. The bent or damaged part may well be knocking now because it is bent or broken.
Alternatly, an accessory like the power steering pump might be causing a knocking noise and causing the belt to drag and squeal.
Try this.... remove the belt and start the engine. It's safe to run it for 30 sec or so with no belt. Does the knocking go away? If yes, a belt-driven accessory is bad. If the knock is still there, the engine may be damaged.
Also check the engine and transmission oils Do they look good or milky/frothy. If it's the latter, water has contaminated the oil. Such water-contaminated oil can also cause engine damage and odd noises, but usually after a fair amount of driving.