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Dry river channels on Mars suggest that water flowed over the Martian soil at some point in its geologic history. If this was the case, the atmosphere would have had to have been much thicker, and the temperature would have had to have been warmer. But somehow, this water was either permanently frozen underground or disappeared in some other way. If the meteorologists can determine exactly what the reason for the this disappearance was, they can possibly find water deposits on Mars, or try to reverse what happened.
Another thing that they study are the dust storms that frequently move across the Martian terrain. They are very concerned with these storms, since they are a constant threat to the lives of the colonists. So far, the only defense they have against these storms are tall windbreaks at the perimeter of the colony. Studying the weather on Mars also helps meteorologists understand weather on Earth.