That crystal clear water sure looks inviting, doesn't it? Of course, it's not always like this...
Dirty water can be a deterrent at first, but it doesn't have to be. Sure, there's a point where the water might get just too muddy to fly fish effectively, yet in all but those toughest conditions success can still be had. The trick is to not just be prepared gear-wise, but to also know how to handle these demanding conditions.
Here's a few tips I use when fishing in dingy water:
Fly Size/Bulk: The dirtier the water, the more attention the fly needs to attract. This can be achieved by increasing the fly size and choosing one that's bulkier. Picking a bigger fly means it will have more presence underwater and can both be seen and felt easier. Likewise for a fly that's bulky. An old-school example of a bulky streamer would be a Muddler Minnow that's constructed with a spun deer hair head. As it's pulled along, that bulky head will "push" through the water as opposed to something like a standard Woolly Bugger that just kind of slips through the water with its more streamlined profile.
Make Some Noise: Ever seen a conventional bass angler fishing in dirty water? In conditions like that, noisy baits such as rattling squarebill crankbaits and jigs, or texas rigs that use a brass weight coupled with a clacking bead can be extremely effective. Can those offerings still work without the added acoustics? Yes, but that touch of added noise and attraction can go a long way in less-than-ideal water clarity. Similarly, many flies can be constructed with the addition of a small rattle chamber tied onto the hook shank. A rattling fly may not be as noisy as certain conventional baits, but it's better than no noise at all!
Colors: I keep color selection pretty simple here. Black or purple are two personal favorites that have worked really well for me over the years in water ranging from off-color to muddy. These two colors contrast well in dirtier water and give the fly a nice silhouette that can be seen more easily. On top of this, these are more natural colors so the fly will not only be easier to see, but will still look realistic, too.
Where/Speed: The dirtier the water, the slower and more methodically I fish. With the poor visibility (and often colder water), I want to give the fish ample time and opportunity to encounter my fly. I'm picking apart the water methodically by fishing areas very thoroughly and making multiple casts around key structure, cover, slack water, and other high-percentage holding zones—no matter how small those may be. Be on the lookout for pockets of slightly clearer water and any break in current. When rivers and creeks are high, species like trout stick to the bottom and may seek refuge along undercut banks that offer less current to fight against.
There's a few positives about fly fishing in murky water....
Reduced visibility means you can tie on a heavier leader/tippet if desired, but remember that a heavier leader means your fly will sink slightly slower. If you use fluorocarbon a lot when the water is clear, you can save that expensive stuff and just use regular monofilament in these dirty conditions. Fish will also be less prone to spook as easily because of the poor visibility and higher and/or swifter water levels, so you may be able to get closer to the fish and won't have to worry about soft presentations.