Lakes and reservoirs integrate the hydrological processes that occur within the upstream watershed.  The effects of wildfires, mining, urban sprawl, and atmospheric deposition within a watershed are identified using analyses of lake water and sediment samples. 

With calm lake waters and warm water temperatures at the lake surface during summer, biological activity (phytoplankton growth) can occur rapidly, making for good fisheries as well as providing organic matter for the lake bottom.  Phytoplankton blooms die off during fall and winter, leading to chemical conditions at the lake bottom that might be "swampy," and when the lake "turns over" sometimes you can smell sulfide gases that have may have been trapped at the bottom of the lake by stratification.

Lakes can also concentrate mercury and other trace metals from atmospheric precipitation that falls directly on the lake and within the watershed.

There are a number of approaches for lake water-quality problems:
--Lake water-quality sampling
    -Trace metals, nutrients, and dissolved organic carbon (DOC)
    -Lake-depth profiling for temperature, pH, specific conductance,
      and dissolved oxygen
--Upstream watershed source sampling of water and sediments
--Stream gaging of inflows
--Lake sediment sampling for age dating
--Reservoir modeling of inflows and water quality
--Reservoir aeration for public water supplies

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