There’s a pretty varied set of [indicators](https://www.epa.gov/national-aquatic-resource-surveys/indicators-used-national-aquatic-resource-surveys) that are used to characterize bodies of water.
The main classifications are biological, chemical, and physical.
In the simplest terms, though, clear water has less in it, as EspritFort suggested.
Different bodies may have different levels of biodiversity, dissolved compounds, suspended solids, or activity.
The size of any particulate also plays a role, with smaller particles being disrupted and dispersed more easily and settling more slowly.
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