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Thanks Lisa. It so green on top now... I'm worried the green algae will make it's way into the pond itself!I'm gonna agree with more plants. And yes, your gravel won't always look "pretty" but if you have enough plants you won't see it anyway.
It's interesting that the string algae is popping up in an established pond, but you did do a lot of stirring up with all your reconstruction and plant removal so it makes sense. I wouldn't blame the bog for the string algae developing - when I get it, mine always grows on my waterfall. Does it like moving water? Is that where the nutrients are gathering? Not sure. And your bog is so new that the bacteria hasn't really had a chance to colonize yet... I think it needs more time to mature.
Your bog also functions a bit differently in that it's more a mixing of bog and pond water than a waterfall or other outflow, so it will be interesting to see how it develops. I've seen the in-pond style of bog used successfully in swim or recreation ponds, so they definitely work.