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I only have a 5g tank, so my siphoning and refilling doesn't take the time and effort it would for a larger tank...and I'm sure my methods would change slightly if I had more water to change. Right now, since I'm still cycling, I use the tube from my gravel vacuum (but not the vacuum itself) to siphon off the water I'm going to change.
1st - I fill a second bucket with my new water and condition it.
2nd - I turn off my filter, so it doesn't stop and choke on itself when the water level drops. This is a pretty fast process for my small tank, so there's no worry of anything drying out...plus, with how I add the water back in, there's really no harm being done.
3rd - I siphon out the old water into another bucket. Both buckets have lines on them to mark certain volumes of water so that I'm sure I have an equal amount in both.
4th - I use a cup to scoop and pour the new water from its bucket into the filter/bio-wheel so that they stay wet, catch any small debris that might end up in the water (like hair), and the flow created in the tank is a similar rate and in the same place as it is with the filter on, so there's no abnormal disturbance to my decor or fish.
5th - I turn the filter back on.
This method is working very well for me so far, and has made my daily water changes a relatively quick and easy process.
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