With this many rivers and lakes nearby, the real question usually isn't "is the fishing good here" — it's "which water actually fits what I want to do." Here's a simple way to think about it, based on what you're after.
If you want the classic Montana fly fishing experience: Head to the Blackfoot River. It's the river fromA River Runs Through It, and it's still one of the best places anywhere to learn fly fishing with a guide. If you've only got time for one river near Missoula, this is a strong pick.
If you want a relaxed day, wading or floating: The Bitterroot and the Clark Fork are both excellent, approachable rivers close to town — good for a laid-back day on the water, whether you're new to fishing or just want an easy outing.
If you want a serious trout stream with a real reputation: Rock Creek is one of Montana's official Blue Ribbon trout streams, known for its healthy population of wild trout. It's a smaller stream than the Blackfoot or Bitterroot, and it draws anglers who take their fishing seriously.
If you want a shot at something big: Flathead Lake is enormous, and the lake trout in it can be enormous too — the state record caught there weighed over 42 pounds. It also has hefty mountain whitefish and year-round trolling charters, including trips through the winter.
If you want variety in a single trip: Salmon Lake and Seeley Lake both mix strong trout fishing with hard-fighting northern pike, so you can switch things up without switching lakes.
If you want to fish through the winter: Flathead Lake runs charters nearly year-round, and Georgetown Lake is a solid pick for guided ice fishing. Salmon Lake and Seeley Lake are also popular ice fishing spots — Seeley Lake even holds an annual "Pike On Ice" tournament — though most anglers there fish on their own rather than with a guide.
However you like to fish, there's a water near Missoula built for it. From here, take a look at how to pick the right guide for your trip, check the best time to fish for your plans, or compare local outfitters directly. You can also head back to the fishing hub any time.