Project: Murky Waters (WisconsinWatch)

The Capital Times and Wisconsin Center for Investigative Journalism collaborated on a four-part series to examine threats to the quality of the Madison area’s spectacular lakes, and ambitious new efforts that seek to improve them. 

Part 1:

WisconsinWatch

WisconsinWatch

The Yahara lakes — Mendota, Monona, Wingra, Waubesa and Kegonsa — are no clearer than they were 30 years ago, despite intensive efforts to improve them. During that time, lake scientists said, the increased heavy rainfalls that are part of climate change most likely offset gains from better land use practices, by washing giant volumes of pollution into the lakes.
“They are flatlining,” said Steve Carpenter, a University of Wisconsin-Madison professor who has studied the Yahara lakes since the 1970s. “There are no trends in the lakes. The lake water quality is not getting better. It’s not getting notably worse. It’s as if the interventions we’re doing are just holding the line, running in place like the red queen in Alice in Wonderland.”
— http://www.wisconsinwatch.org/2014/04/23/yahara-beach-closures-highlight-algae-bacteria-threats/

Part 2:

Mike DeVries -- The Capital Times

Mike DeVries -- The Capital Times

According to experts, agriculture accounts for roughly 70 percent of the phosphorus runoff in watersheds across the state, with urban runoff accounting for the remaining 30 percent.
It is closer to an 80-20 split in the Yahara Watershed in Dane County, said Carpenter, who hopes to find a way for the dairy industry to thrive while protecting water quality.
The agricultural runoff that often turns Madison’s lakes unpleasant by creating algal blooms that look and smell bad, clog boat motors and close beaches is expected to only get worse.
— http://www.wisconsinwatch.org/2014/04/30/manure-digesters-seen-as-best-hope-for-curbing-lake-pollution-but-drawbacks-remain/

Part 3:

 City of Madison Engineering Department

 City of Madison Engineering Department

A Milwaukee scientist who has found sewage migrating from old pipes through soil and into the stormwater lines that drain to lakes or streams says the problem is likely to occur in Madison and cities nationwide.

“In any urban area, this is going to be an issue,” said Sandra McLellan, professor and senior scientist at the University of Wisconsin-Milwaukee’s School of Freshwater Sciences.
From 2008 to 2012, McLellan and colleagues from her laboratory analyzed more than 1,300 water samples from stormwater outfalls in six Milwaukee-area watersheds, looking for a bacterium called Bacterioides that indicates the presence of human sewage...

They found the marker in every watershed. In the Menomonee River watershed alone, more than half of the outfalls were chronically contaminated with sewage.
— http://www.wisconsinwatch.org/2014/05/07/leaky-sewer-pipes-could-export-viruses-to-lakes/

Provided here to explain consequences on lake water quality, a lot of information is.  Hmmmmmm.