Wow, this was really confusing to me. I know that at Lake Powell, cliff diving (over 15-ft) is illegal. Also, scuba diving in marinas and at launch ramps is illegal. But that's about all.
I searched the web, and found lots of unofficial (i.e., not US Gov't sites) talking about scuba diving. Since I could find anything official, one way or the other, I called the Flaming Gorge District Ranger, Manila, UT office and asked. The lady who answered the phone said there were no restrictions. When I relayed what R0gue above said about the visitor center person, she put me on hold and checked with the District Ranger himself. No restrictions on scuba diving. She did say that if you parked or possibly even entered or exited the water from one of the designated swim areas, then you would have to purchase the requisite Recreation Pass.
I'm not that familiar with the area, but it is prudent not to dive, without permission and surface support, in a Marina or at a launch ramp. The Federal Regulation prohibit diving in areas where it is not feasible for routine vessels to abide by the regulations to keep clear of scuba divers.
As an aside, I a couple years ago I found a group of divers who tried to close the whole Escalante River arm at Lake Powell by placing dive flags about 50-ft apart across the river. They left them whether there were divers in the water or not. Clearly, that didn't last, and they were prohibited from continued diving in that area.
