If you're floating the line above them, on the surface of the water, things get worse. Now they see the depression of the water surface, as well as the shadow and the movement. Sure, you can see that a bright orange line is orange and a green line is green, but you won't find either line acceptable. But which colors are the best? Remember that a fish looks up through the water, which is a completely different view from yours looking into the water.
Lately I've been playing with various colors and I like tan, cream, light green, light brown and gray. For everyone, I like gray and light green better. In most fly fishing applications, the color of the line doesn't matter. If the cast is properly presented, the fish will only see your leader.
Occasionally, when fishing for species with exceptional eyesight, you'll need to adjust the length of your leader and possibly the color of your line. We may want to take some ideas of flight line colors when observing nature. Almost all wild creatures survive in part thanks to their natural camouflage. Most fish and birds that can be seen from above and below have a lighter color on the belly than on the back.
This is because when you look at the sky, lighter colored objects are more difficult to see. When viewed from above, darker objects blend into the background. When I entered the field of selling sporting goods in the mid-1970s, fly line manufacturers were more interested in making lines visible to anglers than hiding them from fish. For example, the Florida Keys have become a world-renowned fly-fishing destination for tarpon and permit.
It's strange that so many fishermen want to be known as innovators, but they hate to look different while fishing. If you're new to fly fishing, selecting a two-tone line will help you learn the mechanics of the cast. As both subspecies of rainbow return to rivers to spawn, their colors change to more earthy tones, making them more difficult to see against the bottom structures of shallow rivers. On the other hand, what is the drawback of having a more natural color line that mixes with what a fish sees around it? We know that fish see colors.
When fishing in clear tropical waters, I would highly recommend the Cortland Tarpon Taper Clear fly line. Since fish have limited visibility in these environments, you'll need to place the fly closer to the fish to ensure it will be discovered. Although there are situations where special attention should be paid to the color of the line, most often it does not matter. Bert said he had caught a lot of fish with his two-fly platform, but most were landed with the Skunk fly, maybe only one in ten took the Cigar Butt.
Being able to see the fly line will help you have a frame of reference as you learn to read fish and drifts. If you were fishing for tarpon in clear water or with a hunting permit, I would highly recommend the use of transparent fishing line.