I have a skimmer with a matala pad so that helps catch some of the doodles. During this time of the year, I also try to get my net (skimmer net with very fine mesh) out and get as much of them out as I can, before they have a chance to possibly sink. I have a drain pipe at the bottom of my waterfall filter receptacle, so it is very easy for me to do small water changes. I don't really know if it makes that much difference, though. Using a carbon filter, as others have suggested, might be more effective. I think the most helpful thing is to prevent stuff from getting into the water. In the fall, I use a net for leaves. In addition, I have covered the top of the net with tulle to keep acorns from falling through. It looks ridiculous, but the year I didn't do it -- I had major regrets. (Mostly while standing in cold water and trying to hand collect a gazillion slimy acorns from the bottom of the cold pond.
One plus with the tannin-darkened water: it makes beautiful reflections!!!!!