I'm note sure how much time you've got to travel, but if you've got enough time to visit Tofino I'd highly recommend it. Tofino is located on the West side of the Island at the furthest North end of the road. I believe it's approx. 3-5 hr. drive from Vicoria. You'd probably want to spend the night if you make the trip. I did a half day trip out of Weigh West http://www.weighwest.com/ to fly fish for Coho. Our guides name was Karma. Great guide and lots of fun.
I'd have to second 7x's reccomendation, with just a couple caveats. Tofino is every bit of 5 hours by car from Victoria (but worth the drive). Weigh West's flyfishing program is about the only way to go, unless you have your own boat. There is extremely limited shore fishing opportunities at Clayoquot Sound, as it is eseentially roadless. I believe Weigh West is still open by end of Oct, and their prices are reasonable. However, weather can be iffy on that area of island by then, and fishing will be winding down but should still be good. I've been going every year for the past 6, usually in Aug or early Sep, for feeding coho on the outer Sound. Been interested in going late, hear it can be good, but slightly different, for local fish in the interior. Clayoquot is beautiful, mostly uninhabited, definitely worth the trip.
Oh yeah, Karma is a great guy, and a great fish-master.
I just got back and had a *huge* blast on the Cowchin river. It starts at Duncan (north of Victoria, on the east side) and goes up to lake Cowchin.
We camped at the Stoltz pool campgroup for like $10 Canadian a night. It wasn't crowded, and the weather was darn nice. As for the fishing...
I drifted some eggs and a couple of nymphs and ended up with pretty good results. The first day I caught only 3 fish (one 12" jobbie, 2 littln's). But on the morning of the 18th, I hooked into 5 trout (browns and rainbows) in like 30 minutes, none of which were smaller than 14" (*not* a joke, I've got photos!).
It's kinda an urban river, near towns and such, and the regulations are a bit tricky, but it is a really neat place.
Just returned from Victoria, BC
lower Cowichan occupied by tribals killing salmon from the bridges with spears... so I decided to concentrate on trout
Fished couple of well-known sites upstream from Duncan (Sandy pool and Skutz falls area)
Kingjamm You'right river holds decent trout I hooked at least 12 incher but not landed :-(
I'm pretty sure I saw your campground near the riverbottom road
The thing I like there is not too much angling pressure as in Washington... in spite of close distance to urban areas