Guys, I've been enjoying the discussion and the various theories on the declining fishery. I think I can add something to the pollution angle.
I've been lake sampling for the University of Missouri "Lakes of Missouri Volunteer Program" for going on 10 years now. From April to October I take samples and water clarity measurements at K dock and the mouth of Mincy Creek. The labs measure nitrates, phosphates, and chlorophyl (algae estimate). Believe it or not, there is a definite trend of cleaner water during this time, especially since 1999. In fact, since 1992 the levels of nitrogen and phosphorous have never been lower than from 2003 to present-day.
This trend is mirrored with Taneycomo, and is generally believed to be linked to improvements in the Branson treatment plant.
So, anyway, this study wouldn't capture all pollutants, but for sure it rules out sewage. In fact, some might speculate that the reduction in algaes below a certain level is not good for fishing (bottom of the food chain and all that).
Carry on!