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Everybody always says that dirty water stays warmer, but I almost always on these lakes find it opposite in the Winter time, with the main lake clear water a tad warmer. I guess you can attribute that river water being colder to not as much of it and it being shallower (relative) it will cool faster on those cold days of - degree temps.

There are 2 reasons why everybody says dirty water is warmer. One reason is the water may be stained or dirty because of runoff, which in the Spring can be rain that is typically warmer than the water and it also can be warmed by ground temp or sunlight as it runs in to lake. Theoretically, dirty or stained water will warm quicker and stay warmer because of the particles in the water that absorb heat directly from the Sun or from air temp. On the other hand, clear water runs deep. In the deeper areas, as the top layer cools, becomes denser and drops, the warmer water from underneath replaces it.

So, you are correct in your assumptions that the surface temp of shallower water can actually be colder than deep water.

In the Spring, it can be just the opposite.

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