Open sea I don't think it makes a bit of difference really, subsurface.
Estuaries, its often only a few days after the main rain occurs that they fill up with freshwater. It probably depends a lot on the estuary currents, bars, swell (if any) and how much the fresh and saltwater get mixed together as a result. If there is little disruption to the flow of outwards freshwater, then it will sit above the saltwater below it - so in theory the deeper, lower layers could well be almost unaffected (and still properly salty) (time for diving lures of softbaits?!). Tide ebbing... tide flooding.... I know the local estuary here doesn't fish too well when it's been full of freshwater. Fine for flounder, but not too much else. Saying that, bass get caught literally miles upstream and are one of the few species round these 'ere parts that can cope quite nicely in freshwater. The bad fishing probably has more to do with the fact that the extra water is either a) pushing the smaller baitfish (etc.) further out to sea, or b) that the increased amount of sediment coming down the river is just generally making the fishing harder?! Blimmin hard to know really. I would say that it just as probable that the food source doesn't like the extra moving fresh water as it is the bass don't like it. I think there's often quite a long chain of events with things like this and the answer will pretty rarely come from the fish we're actually looking directly at.