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A question I am often asked is if a water change can be done during a cycle. A lot of aquarists get told one way or the other without a reason why, thus get very confused. As usual, it is because of a lack of context. Whether a water change should be done or not really depends on this situation. However as the recommendation is passed on from person to person, usually the original (valid) reason is lost or distorted.
Here's a list of when to and not to do a water change during the cycle. Before that though, one thing I have to say is - yes, you can absolutely top up your tank during a cycle. This bring zero harm whatsoever. Oh and, here's a refresher on how to cycle, if you need it.
When to do a water change
To keep your live stock safe during a fish-in cycle. I have this as the top reason because it is extremely important. When you are cycling with live stock, you just need to keep them healthy, that's it. You may ask - what if there is not enough ammonia and nitrite to feed the nitrifiers? First off, any amount of ammonia and nitrite is enough, it does not need to be at a certain concentration. Secondly, even if ammonia and nitrite reads zero, it does not mean there is no ammonia and nitrite available for the nitrifiers. Fish (or other live stock) will produce the ammonia necessary anyways, likely throughout the day. After all - if you think about it, that is exactly what is happening in a cycled tank.
To remove contaminants from the water. Whether it's soap or anything else that may have contaminated the water, it is good to do a water change to get rid of it - not only to prevent damage to the beneficial microorganisms we are growing, but for the long term health of the tank too.
To lower ammonia and nitrite to 'safe' levels. Let's be clear here, this is absolutely not a ticket to rely on water changes to zero out ammonia and nitrite during a cycle, and I will explain why later. However, if ammonia and/or nitrite concentrations get too high during a cycle, it actually deters the growth of the beneficial microorganisms we want to grow, so there is a reason to do a water change to reduce these parameters. Dr. Tim suggests not letting either ammonia or nitrite to 5ppm, which is a decent target to follow for one reason: it is quite easy to determine whether your ammonia and/or nitrite has hit 5ppm. However, I have found that concentrations much higher than 5ppm is needed to really even start inhibiting the cycle, let alone stall it completely. My personal recommendation is around 16ppm for ammonia, and 40ppm or so nitrite. It is up to you when to do a water change here. Keeping ammonia and nitrite below 5ppm at least will not harm the cycle, so if it gives you peace of mind, you can keep ammonia and nitrite below 5ppm.
To balance out parameters. A cycle is not a process that occurs in a vacuum, and yes, the beneficial microorganisms we are cultivating can affect water parameters (beyond ammonia, nitrite, and nitrate) in various ways. Whatever reason, parameters can be significantly off, and a water change may re-balance parameters (such as pH). With that said, I would suggest figuring out why parameters keep on changing, and fixing it long term if need be. For example, you may want high pH (8+) for african cichlids, or low pH (6.5-) for ram cichlids, so here we'd need to figure long term ways to keep pH at the target level.
When to not do a water change
Just to get ammonia and nitrite to read 0. Okay, let's think very carefully about this. Yes, part of what we want to see during a cycle is that ammonia and nitrite reads 0. However, we want to see that as a result of nitrification, not because of our intervention. So we want to let ammonia and nitrite naturally be consumed if possible.
When you just dosed the tank with nitrifiers, as that can remove them before they have a chance of colonizing surfaces in the tank.
That's all. So yes, otherwise you can absolutely do a water change, but if not for the 'do' reasons above, it is just a waste of time, effort, and resources. But that's why I have to say this, and loudly:
Water changes do not harm the cycle!
Not directly anyways. You are actually removing some beneficial microorganisms living in the water, but not really anything significant given the bulk lives on surfaces. So everyone that say your water changes are not removing your beneficial microorganisms... well, for all intents and purposes, they are right! Again, except if you literally just added nitrifiers to the tank - then you'd want to wait perhaps 24 hours or so just to give time for them to settle down.
You do need to account for your changes in ammonia and nitrite if you do do a water change though (whatever the reason may be).
For example, you currently have 2ppm ammonia in the tank and you do a 50% water change, for whatever reason. 24 hours later you read 0ppm ammonia. This did not mean your nitrifiers consumed 2ppm ammonia in that 24 hours, they only consumed 1ppm. Very important especially towards the end of a cycle when you may start to consider doing a water change say to lower nitrates.
Well, that's all! I hope that helped clear up some confusion for you. As usual, if you have any questions, don't be afraid to let me know!