Just tell him or her you're stepping through, and if they'd mind if you worked your way along below them... 99% of the time they're ok with it if you're polite and ask...
In the case of flyfishers:
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If I run across someone flyfishing and I'm using my gear rod, I always say hi, and ask permission to fish above them...
Never ever step into the river below a flyfisher unless you ask first. I normally call out to a gear guy to step in above me instead, that I'll be done in 15 minutes, and they can have the whole run when I'm done. Every time I say that, they're ok and move upstream from me.
If gear fishing, I always leave the hole and go elsewhere if the flyfisher is working the hole more slowly than I'd like. I rarely even bother asking if I can go below, unless they are not moving at all.
If they are not moving and I want to fish through, I ask them if they're stepping through, and ask to fish below them; I do so quickly and leave.
Spey fishers need a good 30-40 feet of space downstream of them to cast, so factor that in, and keep moving out of the run if you are given permission to fish below.
There's lots of places to gear fish that flyfishers can't, so I mostly leave them the water if they were there first.
Cheers,
Nicole