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Cloudiness from a mud substrate takes forever to go away, in my experience. I'd definitely go ahead and run the filters, and I'd suggest doing big water changes to hurry it along. Just be careful not to disturb the substrate too much when you're adding water back in, else you'll be back to square one, or worse off than when you started.
 

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Mine is still a little yellow and cloudy after a three days, and I did about 3 50% water changes, filter running the whole time. The cloud is so fine, I'm not convinced any amount of normal filtration would un-cloud it. I think the kind of soil used effects this as well. In my tank, it's more of a stained water than a cloud, but it's really starting to look nice on day three. I'm thinking one more water change and one more day mine should be perfect.
 
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