Is filtered water really a better choice for aquaponics? Doesn't my well water have all the nutrients and minerals that I am going to need for growth? These are some of the questions that I had when putting my system together as well and now that I have been running for almost a year I have learned a few tricks on the matter. I originally thought that the best source of minerals and nutrients to supplement the system would come from my well water. Over the course of the last year I have found this to not be entirely true and also, the well water causes more pH issues than it is worth. Now, don't get me wrong, I am not saying that you cannot use well water here. There is definitely a way to get around the pH issues and top off the system with your local well water. It is also important to note that not all well water is the same, it depends greatly on where you are in the world.
In my case the main issues was the presence of a large amount of carbonates in the well water. If you are unfamiliar with the concept of carbonates I have more info in another video here - http://youtu.be/NSXmwaPBQp8. What the carbonates were doing was not allowing the pH in the system to drop below 8. No matter how much acidic solution I added to the system the carbonates would continue to buffer the pH back up. I also had some issues with this same concept due to the river rock that I was using and have recently corrected that as well.
The bottom line here is that although you can use well water in your aquaponics system you might be better off installing even a simple inexpensive filter to at least get rid of some of the carbonates. You can still supplement nutrients if needed but in most cases this is not normally necessary. Using filtered water will allow you to have more control over the water quality and bring the pH into the perfect range for both your fish and your plants.