It appears that the answer is yes. If you spend any time on Westfly, Silver Creek, or a number of other Idaho streams, you may have run into "Whitefish Ed". Ed did a personal investigation regarding the affect of quickly changing water levels on the SFB and juvenile trout. What he found: lots of dead rainbow trout. Before looking at Ed's study I never read too far in to what effect these fluctuating levels were having on the fishery (other than how the river fished). If you care about the South Fork of the Boise take a look at this blog post and Ed's thread on Westfly. This provides some definite food for thought and possibly some reason for change. Either hit the hyperlinks above or copy and paste the links below.
http://www.southforkboise.org/?p=1036
http://www.west-fly-fishing.com/forums/ubbthreads.php?ubb=showflat&Number=689991#Post689991
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