Fluorocarbon has four main advantages over nylon monofilament.

The one that everyone mentions is visibility and refractive index. Fluorocarbon does have a refractive index closer to water and if that were the only factor in visibility, it would be less visible. There is also color and sheen. A line that is the same color as the water is less visible because of the camouflage effect. Sheen is reflectivity due to the oily lubricant that is on the line surface due to the extrusion process of manufacturing. In very clear and thin water, this sheen can spook fish and that is why fly fishers will use Snake River Mud to remove the sheen and oily coating from both nylon and fluorocarbon tippets. All things equal and in clear still water, fluorocarbon is less visible than nylon.

Seeing is believing.

Here is a visual test of 0.16 mm nylon monofilament on the right and 0.18 mm fluorocarbon on the left. The fluorocarbon is THICKER than the mono.

You decide which on is more or less visible. You decide whether the visibility is due to the difference in reflection or refraction. Are you seeing the mono because of sheen from the surface or because it bends the light from behind it differently that pure water, and are you are seeing a difference in DENSITY of the mono vs the fluorocarbon?

http://www.youtube.com/watch?v=YpgGfm6Q0rY

Fluorocarbon's second advantage is that it does not absorb water and nylon does. Nylon monofilament can absorb 10% of its weight in water and loses 25% of its breaking strength.

Fluorocarbon's third advantage is that it is solid and nylon monofilament is porous so for a given volume, there is more material in fluoro line. Therefore, for a given X size, flouro has the potential for being stronger than mono. Check out the line strength ratings of Rio mono vs fluoro tippets and you will see that the fluoro is stronger than the mono. The "rio" difference though is in wet strength. Mono will get weaker and fluoro will maintain its strength. The absorption of water by mono also weakens the mono knot including the tippet to fly knot.

Fluorocarbon's fourth advantage is that it is more abrasion resistant. It is harder than nylon. So for nymphing; the wet strength, low visibility, and wet strength makes it better than nylon.

Fluorocarbon's fifth difference is both an advantage and a disadvantage. Fluorocarbon is resistant to UV light breakdown so you can keep a spool of fluorocarbon for years and it will not degrade. Nylon mono gradually weakens. For salt water fishers, that means you don't need to replace the line on the casting reels every year. For fly fishers, you can buy large spools of fluorocarbon and use it over many, many years.

The slow breakdown also means that it stays in the environment for thousands of years. But nylon is not that great either. Nylon mono takes 500 years to completely break down so you shouldn't toss either along the stream or lake.

Although fluorocarbon is a bit denser than water and has a higher specific gravity than nylon mono, nylon is also heavier than water. It turns out that the slight difference in specific gravity has little effect on the sink rate of fluorocarbon vs nylon of the same diameter. Although both are heavier than water, the surface tension of water allows both nylon and fluorocarbon to float and be used for dry fly leaders.

Once under water, fluorocarbon will sink a bit faster than nylon but that does not mean it can break through the surface tension. Tests have shown that fluorocarbon is not dense enough to sink on its own.

We have seen the experiment that demonstrates that surface tension can float a sewing needle on water. But once you push the needle under to break the surface tension, the needle sinks.

The Floating Needle. - YouTube

Surface tension will float also fluorocarbon. But once pulled under water by the fly or split shot, it sinks. If you want to keep it floating longer, coat it with silicone floatant.

The truth is that fluorocarbon will not make dry flies sink NOR is it measurably better than nylon in getting nymphs to sink. Both statements are wrong. Surface tension is what floats both flies and leaders that are heavier than water and lead or tungsten is what makes nymphs sink. Over the average cast and drift, whether the tippet is nylon or fluorocarbon has no effect on making a dry fly float or making a nymph sink.

"The actual blend of polymers used to produce ?nylon? varies somewhat, but the nylon formulations used to make monofilament leaders and tippets generally have a specific gravity in the range of 1.05 to 1.10, making them just slightly heavier than water. To put those numbers in perspective, tungsten?used in high-density sink tips?has a specific gravity of 19.25."

"Fluorocarbon has a specific gravity in the range of 1.75 to 1.90. Tungsten it ain?t, but it is significantly more dense than nylon. But is it sufficiently dense to quickly and reliable break surface tension and sink all by itself, even at zero contact angles, and even in the smallest diameters? No, it?s not. Our testing reveals that most brands of fluorocarbon tippet material in 0X to 8X diameters are no better than nylon at breaking surface tension and sinking on their own."

It used to be that fluorocarbon was stiffer than mono for identical diameters and so it hindered a drag free drift. Now there are limp fluorocarbons so there is less difference between the two. When I buy fluorocarbon tippet material, I buy the limpest one on the shelf. I will give up some breaking strength for a longer drag free drift.

Here's the best article on fluorocarbon vs nylon that I have been able to find:

http://www.flyfishamerica.com/conten...arbon-vs-nylon