If waltz you mean Vienesse Waltz, the music is very similar... I would say that Mazurka's tend to be a little "livilier" more of a "bounce" to it than the stereotypical Vienesse Waltz piece of music usually has.
The dances differ in steps and direction/method of travel. Vienesse Waltz is a rotational waltz (at its root, modern Vienesse has moved away from this some with large amounts of open figures and straightline travel), where the first step is an angled step which starts the bodies moving in rotation, the leader rotating "around" the follower, then the follower rotating around the leader. The Mazurka uses a straight sldiing step as it first step, the second step is a "cut" (sort of a kick-replace deal), the third step is a rotating "hop".
Mazurka is a little more of a jovial dance than the Vienesse Waltz. To confuse the issue there are several dances that use mazurka and Vienesse together or mazurka and polka.
I'm spending ten hours a week for the next month and a half doing Vienesse and mazurkas (with the occasional Schottiche and polka thrown in). I've been working on them myself, after a little bit of exposure hearing the difference in the music becomes really easy.