I don't know aurdino but this is fairly easy to do on the processors I work with.. The answer is the timers.. You can program your GPIO to toggle at a specific frequency using timers.. On the arm processors we use, I do it all the time. The problem is that the GPIOs will provide a square clock, if you need sine wave etc, you need additional hardware.
What you can also do is that you can get two timers using GPIO and use a simple or gate to combine the clocks.
You didn't ask but if you want them to be in some sort of phase with each other, you have no choice but to use advanced timer hardware as with software getting exact phase lock would be challenging.