Lots of potential effects, Jesse. Minor flooding/spates are what do the work in streams, creating pools, pockets, etc... -"digging spates" I call them. But I've seen "catastrophic floods" make barren moonscapes out of previously awesome stretches, only to have them re-dug back into trout hotels in subsequent years.
Because of ditching and draining (everywhere a development goes in), many streams are more prone to be "flashy" as water is removed from the surrounding land at a quicker rate, rather than being retained in the land. Habitat too becomes "flashy" -here today, gone tomorrow. Fish populations may adapt, but some level of stability in the system sure helps grow trout.
As you mentioned, flow affects spawning too. Many trout rely on seasonal spates to move into spawning/nursery stretches. But big floods can scour eggs and sweep fry out of nursery water. Each year is different, and you can see where some stability here is made good use of.
In waters with stable flow, trout lead much more stable lives, often living in small home ranges -some even spending their summers in one pool. In flashier streams, trout move like crazy. Summer, fall, and winter create different habitat needs and trout find these, or perish. Trout in many waters may treat an entire watershed like they might a lake -this seems esp so with those big browns.
Individual trout handle high water pretty darn well. And aquatic insects are mobile and fecund and can rebound quickly even after catastrophic floods. One year, we had a nasty flood while I was teaching a FF course. When we went to sample for inverts in a diverse stream (I'd sampled successfully just the previous week), we caught NOTHING! It was scoured clean. So, we had a nice streamside chat about floods, and rescheduled.
Oh...I also wrote an article on high water fishing strategies called "Ain't No River High Enough" in the March/April 2002 American Angler.