Planted Tank Guru
Join Date: Jan 2010
Location: Contra Costa CA
Some substrates need to exist under water for about a month before they are safe to add fish. Most of the time the problem is ammonia. There should be a large colony of many different species of microorganisms in the soil. Sometimes they are not quite the ones that will thrive in your tank, so some die off, and others increase in population. This takes time.
While the substrate is giving off ammonia, run all the equipment. You are also cycling the tank. The bacteria that will ultimately help with removing ammonia from the fish will grow with any source of ammonia, including the ammonia generated in a newly submerged soil.
Not many bacteria live in the water. The actual nitrifying bacteria live on surfaces, such as filter media. There may be a few bacteria in the water, but I have done more than 100% water changes (water flowing in and out at the same time) and not had any problems with the nitrifying bacteria disappearing. Go ahead and use the water, but it is not worth the effort of saving it. Have you been feeding the bacteria daily? They will be growing on the sides of the container you are storing the water in. Feel how slimy it feels? That is the biofilm that the microorganisms live in.
Now, a fully cycled filter is a great source of the correct microorganisms, and is the best thing you can add to a new tank.
Here is what I would do:
1) Put dampened substrate in the tank.
2) Add driftwood, rocks, create hills and valleys.
3) Add just enough water to BARELY cover the substrate, or not even that much.
4) Plant, misting the plants as needed.
5) Put a plate or plastic bag over the substrate and add water slowly. Allow the water to seep in over the edges of the plate and into the substrate. This minimizes the cloudiness. While the tank is filling you can install the equipment.
6) Turn on the equipment, make sure it is all running.
For the next month (about) test for ammonia, and whatever other tests you want. Perhaps GH, KH and pH, maybe nitrite and nitrate.
Here is what you do with the test results:
Ammonia, nitrite and nitrate: Monitor the growth of nitrifying bacteria. The lower the ammonia the faster the first group (ammonia removers) are growing, and the less ammonia the soil is putting into the water. Nitrite may show up for a while. The bacteria that remove nitrite grow slowly. If the nitrite gets to 5 ppm, do a water change. The bacteria do not grow well when the nitrite is over 5 ppm. Nitrate: As the 2 groups of bacteria (ammonia removers and nitrite removers) grow in population they produce more and more nitrate. Depending on how densely you planted the plants may remove some of each of these. When the tests read Ammonia 0 ppm, Nitrite 0ppm and nitrate anything at all, can be quite high, the soil and the tank are cycled. You can add fish. If you will not be adding fish for a few days or longer then feed the bacteria with ammonia, fish food or other source of ammonia.
When you are ready to add fish do a really big water change to get the nitrate really low. Maybe the plants have already done this for you.
GH: If you want to keep soft water fish you will want the GH to be under 9 German degrees of hardness for most hatchery raised fish, or under 5 degrees for more delicate soft water fish. Lower than 3 degrees might suggest calcium or magnesium is in short supply, and you might have to do something about it. For hard water fish over 9 degrees, and up to 20 is fine. Most plants are not so picky, though there are a few...
While the tank is cycling it is OK to see what you might do about a problem GH, see what might fix it.
KH: For hard water fish over 9 degrees, and as high as 20 is fine. For soft water fish around 3-5 degrees is usually pretty good. This is a buffer that stabilizes the pH. Watch to see if your substrate removes the KH. Some do, leaving the water vulnerable to possible swings in pH.
Do not allow either GH or KH to get below 3 degrees while cycling. The microorganisms need some minerals, and will slow or stop if the minerals are in short supply.
pH: Do not bother doing anything directly about pH. If the GH and KH suit the fish, then the pH will probably be fine. If it does vary, then look for a cause (such as a substrate that has removed all the KH)
Post these tests and what fish you want, and we can help if there is a problem with the water:
Ammonia, Nitrite, Nitrate
GH, KH, pH and let some water sit out for 24-48 hours and test the pH again.
It would be interesting to follow the cycle with you, and see how it is going!