Sometimes, brown water is simply discolored water. Nothing wrong with the water quality, but something has stained the water - leaves, tree pollen, pine needles, etc. I deal with this all the time. Partial water changes each week help remove some of the discolored water.
Don't give up on your pond, 2V's. I know you love it. Just now and then there's gonna be a glitch. Once you get past it, you'll enjoy the pond all the more.