The present continuous makes it clear that the action is currently happening, just like in English. From what I have read so far, it is optional and not used as much as in English, so you could just as well use the simple present instead. But the continuous is useful to remove ambiguity and to put additional stress on the verb. Stress is an important thing in Dutch :)
Note that the present simple form would be "Zwem jij?"
In English, there are three reasons to ask "Are you swimming?" 1) Are you walking across the lake, or are you swimming? 2) When holding up and encouraging a toddler to learn the skill 3) When the answer is 'Stupid question. No, you fool, I'm drowning. HELP!". I am pretty sure the intent of thisquestion in Dutch is better expressed as "Are you GOING Swimming?".
"Are you going swimming?" is literally "Ga jij zwemmen?"
My friend (who is a native Dutch speaker) says that it is the context the words portray themselves as.
A fourth situation for this question would be if you're in a swimming pool, not swimming, and can be asked this.