When I clean my filter, here's what I do...
I use a series of (3) 5-gallon buckets to siphon water from the tank and add water back in when refilling. I pace my siphoning so that the last 3 buckets will be used to clean the parts of the filter with aquarium water.
I take my canister filter out and pull the parts out rinsing them in the first bucket, rinse again in the 2nd bucket and then just store them in the last bucket to keep them wet. I repeat this with each sponge, or level of pieces inside as I move forward. I then dump out the dark water in the bottom of the canister, replace all the sponges and filtering stages into the canister, reseal the canister and prime with water from the tank.
I probably don't do this often enough, but I'm only using tank water to rinse things out and remove the extra gunk. Also not letting any of it dry out while you are doing this.
I don't really test my water params ever, but this has never seemed to bother the fish or cause additional blooms.