Your intuitions sound reasonable, as long as the current isn't very fast. Generally, though, moving water tends to be cooler and better-oxygenated than still water, and so tends to become more advantageous in summer, and less so in the spring unless it's actually delivering bait and heat (as mentioned above). the only way to know, though, is to check. Bring a thermometer and check temps in the main basin, mouth of the river, and in the river itself, to see what the variation is like.
Actually, what you're describing sounds not too different from a situation examined earlier this year by @Paul Roberts on The Nature of Fishing channel, in that case following a spring heat gradient between a deeper main basin and a shallow "back bay" area connected by a creek channel: