Captain Aaron Snell Photo
When fishing the salt water flats visibility is everything. If you can't see the fish you don't know where to cast or how to fish your fly.
The glare of the sun makes it difficult to penetrate the water surface. This is why we wear polarized sun glasses.
Another huge factor is lack of light. The clouds cover the sun light and you're in the dark losing color contrast. Dark clouds on the horizon other hand can actually be helpful. They soak up the harsh glare of the sun. Add sunlight from behind you shining towards the dark horizon and bam you have some of the best glare free high contrast light possible.
So don't give in if there are a lot of big dark clouds around. You could just get some time with the best light possible.