As you use your computer the operating system and applications begin to use hard drive space for temporary files and caches. When the temporary files are no longer needed, the OS and programs should delete them but that doesn't always happen. Every once in a while (maybe once every couple of months) I'll realize that my free drive space is much lower than it should be, or the OS will warn me I'm running low of free space. When that happens I restart the computer and usually the problem is solved. Restarting quits all my applications and the OS and the files are removed/pruned. But on very very rare ocassions restarting doesn't solve it. But a safe boot does. To safe boot restart holding the left shift key until the Apple menu appears.
If the safe boot doesn't fix it check to see that all your programs and the OS are up to date.