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If you are going to change the substrate then you will have to start the cycle all over again. And are you planning on capping the dirt with some type of inert substrate to keep the suspended particles down?
I was having an algae problem in my tank and got some advice that really worked:
1. Added 1.5 ml of H2O2 (3% hydrogen peroxide) per gallon.
2. repeat for 3 days.
3. manually clean glass and plants and do a 50% water change.
This worked very well for me. The H2O2 breaks down into Oxygen and...
The highest the pH will get to by adding limestone is 8.3, where it reaches barcarbonate equilibrium. But I doubt it would even get that high, as the closer it gets to 7, the slower the reaction to dissolve the limestone.