The key to catching flounder on rod and reel is to go low, slow and small. Because of their feeding pattern as an ambush predator, you have to go find flounder rather than parking on fishing a hole and letting them roam to you. Work live bait or an artificial lure that resembles either small fish or shrimp slowly along drop off areas with good tidal flow. Work close to the bottom or bounce off the bottom. The slower the presentation the better.
For hard or sandy bottoms, a small lead jig head with some type of plastic or feathery tail bounced slowly off the bottom is optimal. For grassy areas a small shiny lure like a spoon worked shallow along the top of the grass or a weedless soft plastic rigged similar to a Texas rigged bass lure worked through the grass and dropping down into sandy holes or drop offs are best.
Prime daytime locations are anywhere that there is an obstacle for the flounder to hide near. Jetties, oyster reefs that jut out to open water, points where cuts drain the flats merge, pylons of piers and bulkheads along bay front properties are all good locations. The key is to find good water movement flowing over the areas that will bring small schooling fish or shrimp over the ambush point.