If you've never been on a guide trip before, many guides will lay a towel out on the dock so you can wipe your shoes off before boarding the skiff. I wouldn't want to be that guy who starts off the morning by leaving filthy foot prints on the deck of a squeaky-clean boat. That's likely not going to be a great first impression!
Once aboard, many folks will just leave their shoes on all day. After all, they are shoes and they belong on your feet, right? However, if you typically don't fish shoe-less, it might be something to consider. Just to be clear, this can mean barefoot or wearing just socks.
Besides maybe keeping you slightly cooler in a hot climate, not wearing shoes can make you a more efficient fly angler.
On a boat, there are many things for loose fly line to wrap around or get trapped under. Your feet are one (well, two actually) of those things. Shoes don't help the situation. Shoes can have laces, loops, treads, and who-knows-what-else that can potentially catch a fly line, even if just briefly. When a school of bonefish suddenly appears and an ultra-quick cast must be made, the odds of a smooth presentation improve if the area around your feet is free of additional snags—fishing without shoes helps clean that area up.
Aside from fly line possibly catching on your shoes, stepping on the line is a common occurrence. Now of course this can happen whether you have shoes on or not, but the point of not wearing them is so that you can feel the line easier on and under your feet. With no shoes on, I'm able to feel the line instantly and readjust my stance accordingly. The last thing I want is to be attempting a 40 foot cast only to have my line abruptly stop 25 feet out because the corner of my foot was stepping on the line and I didn't know it. DOHH!!
Is it better to go barefoot or wear socks?
I prefer socks for two reasons. First, I like the added sun and bug protection they afford. Second, fly line can loop around and get in between toes and socks prevent that from happening. As long as the socks aren't super thick, you should still be able to easily feel the line on and under your feet. The one big downside to socks is it can be tough to keep them dry if water gets onto the boat deck.
In addition to all mentioned above, I also feel much more firmly planted when not wearing shoes. I don't have the best balance in the world anyway, and standing on a rocking boat or on a small bow casting platform can be kind of challenging at times. Going shoe-less lets me keep a nice flat foot on deck and I can feel edges/contours much better.
Another thing to be wary of is that not wearing shoes increases the chances of injury such as stubbing a toe or stepping on a loose hook on the floor. I always move around a little more carefully without the added protection, but it's all worth it for more quality presentations and hopefully more fish to the boat!
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