Ahh, there's a potential lead. Caching plugins, such as WP-Super Cache, create HTML "snapshots" of your pages when they're visited so that those who visit the page later don't have to wait for the page to be re-processed. It essentially trades increased storage space for decreased processing time when building your pages. If you have a lot of traffic, it can really give your site a speed boost.
After a while, cache files go stale and are marked for deletion. Depending on how you have your setup configured, WP Super Cache should go through periodically and clean out old cache files that have expired (depending on your expiry time). Your cache can also be manually managed from the Contents tab of the WP Super Cache settings page. I wouldn't recommend going through and deleting files directly unless necessary - try using the tools built in to the plugin's admin panel first.
Now, as for the original topic... if most of your media is off-site and this is primarily the plugin you're using, it's likely this is where your storage is going, and it would explain the fluctuations in storage space (gain some when people visit new pages, lose some when the garbage collector goes through and clears out stale files). Still, if you wanna be 100% certain, I'd recommend connecting via FTP to the server and checking the folder sizes.
And if this is really the primary cause, you can try tuning the settings in WP Super Cache to better match your traffic patterns. WP Super Cache, while pretty simple to use, isn't a "set it and forget it" type plugin - at least if you're looking for optimal performance.
I hope this helps!