I'd guess that the flooding has a major part in the lack of salamanders, as does the close proximity to the river. I've never had much luck near rivers (for Ambystomids). I don't know if the river is a sink for adults/juvies, if it's the flooding you mentioned, or if the water level is too high for their burrows, but these habitats haven't been very rewarding for me, though you might find newts in similar areas.
If you want to go look for salamander locations, a good way to find them is roadcruising. In the spring, wait for the first good rain of the year at night (wood frogs will be calling if the timing is right), and drive slow on country roads near wetland. The salamanders will look like little sticks with heads sticking up. Still, it doesn't really help you now though.
The sandy bottom doesn't matter for mudpuppies, but you're not going to find them if there aren't any rocks to overturn. If you really want to find them, you might want to get a good map and drive out to a bunch of bridges, looking for a shallow area with lots of rocks. I've had the best luck in 2-3 feet of water, with rocks over 12 inches in diameter.