This will be a landmark year for the river. Many people may now describe the area in terms of pre- and post-2013.
A wildfire burned through much of the canyon in mid-August, blackening the slopes, scorching the rivers cottonwood stands and exposing thousands of acres of bare soil.
Then, on Sept. 12, a thunderstorm dumped about a half inch of rain on the upper slopes north of the river and caused five mudslides in the prime fishing and recreation area between Anderson Ranch Dam and the Danskin boat launch about 10 miles downstream.
The combination of wildfire and slides have changed the river and the canyon and this could just be the start of it.
After talking to numerous experts about the fires and slides, theres no consensus on what the future holds because the changes are still happening. But all signs point to a long-term recovery.
Using previous fires, even a fairly recent one, as a predictor of what will happen is difficult because of the intensity of the Elk Complex Fire.
Many fires leave patches of areas burned and others untouched, but the Elk Complex was unusually intense, and in many areas, it burned everything in its path.
David Olson, public information officer for the Boise National Forest, said the Elk Complex burned 276,000 acres during three weeks, including 180,000 acres in 48 hours.
By comparison, last summers Trinity Fire in the South Forks headwaters burned 160,000 acres during two months.
The mudslides washed thousands and possibly millions of yards of mud, rock and debris off the upper slopes and down into the canyon, and much of it entered the river.
According to biologists and scientists, the river should be able to clean and restore itself, but that depends on whether more slides occur and whether theres enough river flows to clean out the channel.
Terry Hardy, soil scientist for the Boise National Forest, said several things are currently in play.
The slides that already occurred are more than likely a one-shot deal. They arent going to move on that scale again, but could become chronic bleeders of sediment into the river after future rain storms and snowmelt.
Slides at Rough Creek and above Reclamation Village spread into broad deltas that could be contoured with earth-moving equipment and replanted to reduce further erosion.
Steeper creek drainages, such as Pierce and Granite creeks, could continue to spew mud until they stabilize. Other drainages could still slide, especially with so many slopes laid bare by intense fires.
The half inch of rain that fell last week was not unusual but it fell in about 45 minutes, which is a brief period for that much rain.
Hardy said the burned and bare slopes magnify the effects of storms. For example, a 10-year weather event could have the effects of a 15- or 20-year event, he said.
Its difficult to know how much rain or snowmelt it will take to trigger more slides.
Theres a high level of concern, primarily because weve seen what can happen, Hardy said.
But its possible we could have already seen the worst, he said.
I dont know if there are that many more tributaries that could release and have that kind of an effect, he said.
The river continued to run murky on Monday, but muddy water was also coming out of the dam, which likely came from slides on the west side of Anderson Ranch Reservoir.
Trout are rarely directly killed by mudslides, according to Jeff Dillon, state fish manager for Idaho Fish and Game.
Fish are very well equipped to deal with these things, Dillon said. They happen not every year, but on a regular basis in nature.
The timing of the slides may actually be advantageous in some ways, he said.
If theres going to be a slide, this is probably a better time for it than in the spring when the fish have eggs in the gravel.
The dam also provides a steady flow of cool, clean water downstream. Flows dropped to 300 cubic feet per second (cfs) on Monday, and will likely remain at that flow through winter.
Assuming there arent repeated slides, the water quality will improve very quickly, Dillon said.
Joe Kozfkay, Fish and Games southwest region fish manager, surveyed the river on Monday and said he saw some dead suckers, whitefish and kokanee, but knowing the total mortality from the slides is almost immeasurable.
I still think adult fish mortality is really low, so I dont think we should be panicked, he said.
They found schools of trout younger than a year old that survived the slides.
Theyre the most susceptible, so thats a good sign, he said.
Longer term will depend on what happens next. More slides could make things worse, or a big spring runoff could flush the channel of sediment and actually improve the rivers fish habitat by leaving more spawning gravel.
Kozfkay said the South Forks trout population has been remarkably stable, and thats not likely to change.
Fish and Game surveys the river every three years to monitor it.
I think were OK, but were going to watch, he said.
A short-term flush of the river looks unlikely and will largely depend on this winters snow pack.
The Bureau of Reclamation on Monday reduced flows from 600 cfs to 300 cfs out of Anderson Ranch Dam, and 300 cfs will continue until spring, according to Brian Sauer, hydraulic engineer for the bureau in Boise.
Anderson Ranch Dam is currently 75 percent drained, and it will take a really big water year before we release any more than we have to, he said.
The river has remained largely unchanged since 1996, when a rainstorm on snow triggered a mudslide.
John Wolter, owner of Anglers fly shop in Boise, remembers that it looked like a war zone that year. Big boulders were strewn about and huge trees were scattered around like toothpicks.
That incident formed whats now commonly called Slide Rapid, but the river quickly recovered.
We were fishing the next spring, Wolter said.
But that slide wasnt nearly to the degree were seeing now, he said.
He said anglers need to exercise patience, both in waiting for the river to restore itself and also for the Forest Service to reopen it to anglers.
There are many hazards that must be mitigated before people can return to the river, and hazards will persist as new rapids are formed and logs and debris work their way downstream.
Insects may seem trivial considering all other things affected by the fire and slides, but theyre a major reason why the South Fork has such a healthy trout population.
We should expect total numbers of stream insects to immediately drop along the burned area, particularly in those areas where mudslides have occurred, said Dr. Chris Walser, professor of biology at the College of Idaho and a stream ecology specialist. Other studies in different parts of the western U.S. report that all insect types were immediately impacted by fire.
Walser expects mayfly and midge populations to recover first, possibly within months to a year and potentially in greater abundance than before the fire.
Other insects, such as stoneflies, may need two to four years to recover.
Some scientific studies indicate that it may take seven to 10 years for the stream insect community to fully recover to pre-fire conditions, he said. Length of time depends on many factors most importantly the frequency and magnitude of future flash floods and mudslides.
The rivers large cottonwood groves provided many shady spots for campers, and not only are many of those dead or dying, they now can be hazardous because they may fall over at unpredictable times.
Before the slides, Forest Service crews were working to cut the most hazardous trees down, but it will be a recurring problem.
Cottonwoods are easily killed by fire, and they have a shallow root system that makes trunks unstable after the tree dies.
Some of the campsites were severely burned, but a few around the Indian Rock area were largely unscathed.
Olson said Forest Service officials know the South Fork is a popular area for recreationists, but they have to mitigate hazards caused by the fires before letting the public return.
Most of the facilities along the South Fork, such as boat launches and outhouses, were intact and unaffected by the storms and slides. However, the Tailwaters Campground and boat launch appear to have been damaged by the slides.
The Forest Service has emergency funds for habitat restoration, but improvements to recreation facilities will compete with other projects on the forest, Olson said.
Both anglers who float the river and boaters who run downstream in the canyons whitewater will have to adjust.
The river is currently close to floating by Forest Service order.
Slides have already altered the stream channel, which will likely continue as the river starts flushing itself and rearranging.
Fires killed many cottonwoods and other trees in the riparian area. As those trees fall, many will end up in the river, which could create log jams.
A major log jam formed in the canyon below Danskin in 2006, and floaters had to wait weeks before it was removed. That could reoccur in the spring when high water starts carrying fallen logs downstream.
Boaters will also likely see new rapids emerge and old ones changed after slides pushed boulders off slopes and into the channel and moved others around.
New growth is already sprouting in the South Fork canyon, which is good news and bad news.
Willows quickly regenerate in the riparian areas, and many areas remained green after the fire. Cottonwoods will take longer to regenerate.
Plants that will help stabilize the soil on the slopes need moisture to grow again, but too much moisture obviously creates problems. Among the first plants to regrow are noxious weeds, which can easily spread across the soil deposited by the slides.
Most people think of the South Fork as a fishing spot, but its also an oasis for wildlife and winter range for big game.
In the long term, the canyons plant community may be affected worse than the river if noxious weeds take over, but that may be overlooked by people focusing on the river.
Roger Phillips: 377-6215, Twitter: @rogeroutdoors