I wonder if he has ear mites? Did your vet look down his ears? If you wipe up the black stuff and have a look with a magnifying glass you may be able to see them, if they are there. You can get stuff from the vet that you put into the ears, rub firmly, and it should clear out the gunk. Cotton pads are good for cleaning gently round the top of the canal, but don't poke anything in there.
Ears are so easily infected with spaniels, Milo got infected with ear mites that led to a bad infection and he lost his ear drums and went deaf. When he was poorly I tied his ears up on top of his head to let the air get round them, which helped a bit.
I imagine it's not uncommon in drop eared dogs, ideal place for bacteria. I now check Dylan every day, have a sniff (get familiar with the smell of your dog's ears, bad smell is often the first sign of trouble), I'm paranoid about him going the same way as Milo.
I would just keep them scrupulously clean, and keep him Out of the water. Hope it clears up with no after effects
Lesley and Dylan