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.
Its has to do with the living organisms present, such as in sea, there’s many coral reefs and other creatures that helps to maintain it. Compared to lakes, there’s only fishes which don’t have that much ability compared to corals. We can also account the pollutants, such as oil that contaminates it. There’s many factor, such as soil, the mixing of soil and water will result to darker appearance.
Warmer ocean water generally has fewer microorganisms suspended in it than colder water, which is part of the reason tropical waters usually appear turquoise and clear while the waters off the coast of Maine and northern Europe appear dark and opaque. There are other factors to consider as well such as currents, sediment, and other pollutants, but that’s the gist of it.
I am not a geologist, so take this with a grain of…sand?
This question has mostly to do with two things – particle size, and particle composition. Silt, sand, and clay generally define particle sizes (officially) Sand is coarser than silt, and silt coarser than clay. At the same time, clays are called clays and are fine because of their composition (aluminum phyllosilicates.)
Sands and silt, in the geological sense, are most commonly comprised of quartz and feldspar. These fines are not particularly electrochemically active, which means they mostly get finer via weathering/erosion/fracture and while they can easily be disturbed, they will more easily fall to the bottom of the lake via gravity than clays.
Clays are especially fine, and typically electrochemically active as their mineral structures contain bound water. They usually weather more by chemical erosion – some solvent (including water) can dissolve or react the rock. Because of this, and their electrochemical activity, clays can hydrate, and stay suspended in the fluid depending on its ionicity. This, combined with the fact that they are by definition very fine particles, generally means they stay in suspension and cloud the water they are in.
Most lakes are either cloudy or clear based on two things – their feed sources (Mountainous, rocky, rivers and streams? Plains or basin drainage across grasslands?) and the reservoir itself (does motion of the water stir clays and silts from the bottom continuously? or is the bottom made of larger sand particles or even rock such as limestone?)
If the feed sources contain much silt and clay and the reservoir is small, the water will stay murky as the constant introduction of new particulates (even if it’s quartzy silt) will circulate.
Generally, mountain streams are thought of as clear and clean – they have a very rocky source where snowmelt on rocks feeds the streams directly, and particle sizes are large. So, they stay “clear.”
Compare that to the Mississippi river, fed by so many rivers and streams across mountains, plains, and arable, organic-rich soils, that the clay content and particle sizes present run the gamut – but appear cloudy because the clays stay suspended and the silts are constantly disturbed. This is also the same reason river valleys are so fertile – all the products of erosion and chemical weathering breaks rocks down and alters them into available minerals for plants, which further break and erode rock and introduce carbon, nitrogen, other solvents, etc.
You can also imagine that the mouth of the Mississippi is very rich in these silty, clay-like fines near the ocean, leading to a sort of “muddy” water in the ocean nearby. Contrast that with Palm Beach, which is all limestone karst and doesn’t have sediment flow into the ocean. Add to that the relatively coarse, large sand particles that don’t stay suspended in water for long, and you have a recipe for clear water, all the way to the white sand below. There isn’t much life because there isn’t much organic matter, and that’s because it’s not fed by a source of rich minerals like a river delta.
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