In early October, 2017 a report was released detailing the latest official evaluation of Grand Lake's ongoing (and deteriorating) clarity issues. Grand Lake is Colorado's largest and deepest natural lake. It was (notice the past tense) also famously clear.
Grand Lake is naturally fed by the Colorado, which flows out of Rocky Mountain National Park, and other rivers. That natural inflow is not the source of the clarity problems. As you probably know, much of the water that originates on the west slope of Colorado is actually owned by entities on the eastern side of the continental divide. Water is pumped from Grand Lake through the Alva B. Adams tunnel to Estes Park on the east side of the continental divide. If natural inflows to Grand Lake were sufficient to replace the water sent to the Front Range, Grand Lake would not have clarity issues. Natural flows don't keep up with the demand.
To increase inflows to Grand Lake, and hence availability of more water to the Front Range, a complex system was created. Water is pumped from the Colorado at Windy Gap reservoir up into Granby Reservoir and from there into Shadow Mountain, which is open to Grand Lake. Because Shadow Mountain is shallow and warm, it encourages growth of aquatic plants resulting in pH, DO and clarity changes. Clarity in Grand Lake has declined as a result of it's connection to the warm, nutrient-rich water from Shadow Mountain. Standards have been set at disappointing levels.