Hi Ricker, Bali practically has no flats, there's definitely bonefish there but they all come from deep water netted by the local fishermen.
Freshwater fly fishing is almost non existent in Bali due to many factors, mainly over fishing, pollution, alien species invasion (tilaipia etc) the only thing that somewhat promising is the 'snakeheads' around abandoned ex mining holes. However if you go to the highland, the river might still hold some fish, but don't your hope too high.
There used to be decent fishing near the airport in Bali (around the mangroves) for pacific tarpon and some barramundi but again pollution and over fishing already take the toll.
Saltwater fly fishing in Bali has some potential provided you go to the right place, at the right time/season with the right guide. Trust me on this, because when you have everything all sorted out perfectly it can be heaven. Tuna, Mahi-mahi, GT you name it, a big gun (8wt minimum is almost mandatory).
I'm not a pro guide trying to sell anything, but I've fly fished around Indonesia, so this comes from my personal experience. Now, if you don't wanna limit yourself to Bali, there are other options.
Go for Hampala Barb, giant snake head, mad barb in Borneo. Bonefish paradise in Raja Ampat, mini Maldives in Karimun Jawa, Pacific Tarpon in Batam, options are almost limitless, as fly fishing is a new sport here and new fly fishings spots are being discovered here and there
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