Ryan & ltlCLEO -
Thought folks might have gotten tired of this thread but if you are still interested here is my best shot at your quetions. Some may wish to skip the next 2 paragraphs; doing so would not hurt my feelings, its pretty dry. Salmo G. has done a better job.

Regarding carrying capacity -
Yes, it does seem like Vodoo magic. Values like carrying capacity and the associated MSH point are typcially developed from what folks in the fisheries management field call stock/recruitment (S/R) curves. These typically are based on a time series of information (hopefully over several decades) that includes estimates of the number of spawners and the resulting production (could be smolts, adults etc). These relationships would be valid for the average conditions of the time series. For steelhead management in Washington those curves use number of adult wild spawners and the number of returning wild adults (catch and escapement).

What has been noted is that the relationship between escapement and resulting runs sizes is not linear - in other words doubling the escapement does not mean the resulting run size would double. The reason is that more and more of the habitat is taken the additional fish begin using less adn less productive niches until adding fish over capacity yields no increase in run size. Typically the S/R curves are one of two types (Ricker or Beverton-Holt) and it is fairly straight forward fit the data points to which ever curve appears to best discribe the population. Once the curve is available carrying capacity would be that point where an escapement produces run size equal to itself.

And yes you are correct ltlCLEO that all the above is limited by the quality of the data that goes into it.

A more common sense way to look at carrying capacity is to see how various escapements perform. Escapements above carrying capacity will on the average produce smaller runs, those well below capacity will on the average produce larger runs and those around carrying capacity would produce runs of about the same size.

Lets return to the Skagit example - as mentioned all the escapements above 10,000 have produced smaller runs, all those below 6,000 have produced larger runs and those in the middle have been a mixed bag. This would imply that Skagit capacity would be somewhere between 6 and 10,000. The S/R curves indicates it would be around 8 to 9,000.

Ryan -
Of course having more information from larger escapements would be desirable. If there are only 4 large escapements over 20 years it clearly may take quite sometime to get another 16 points. Since we would need average or better conditions it would likely take 30 to 50 years. The question becomes what to do until then? I think you and I agree the answer is to manage conservatively. I believe the discussion guidelines I proposed did that.

Having fixed low exploitation rates for those runs above MSH does pretty much what you were proposing. With decent survival conditions escapements would be above the MSH point and if runs were larger most would be allowed to spawn thus allowing Mother Nature to care for the population. For example if the run was twice the MSH point and we allowed 20% exploitation then the escapement would be 160% of MSH.

ltlCLEO- Rivers that are functional form a fish's need is a tough one to get ones hands on. For me it a question of allowing rivers to do what rivers should. Historically our rivers have been very dynamic with channal changes, log jams coming and going, etc. Each river has its own characteristics and each with its own mix of fish. Altering flows, constraining banks, etc aren't part of the natural processes.

Prehaps it is important to note that a "non-functional river" with a substanial hatchery program can produce some good fishing and perhaps even better fishing than a functioning river; the Cowlitz comes to mind. The flip side of course is that for some the quality of the fishing is more important that the quantity. It is more important to me to be able to wade a river that is "alive" with a diverse fish resource than to consistently catch fish elsewhere.

Tight lines
Smalma