Both can be translated as "to drink", but "tomar" also means "to take" depending on the context.
For example, a waitress might ask:
What would you like to drink? = ¿Que desea beber? = ¿Qué desea tomar?
The usage of one or the other is indifferent from a grammatical point of view. The speaker might prefer to use one over the other because that verb is more common where he lives.
Personally, I seldom use "beber", I just use it when I want to sound more formal, cause "tomar" sounds more casual and part of the everyday vocabulary to me. But that might not be the case in other Spanish speaking countries, where "beber" is used all the time.