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I want to clean the glass and change some of the water in my tank but I don't want to stress out my larvae too much. I have a berried female and breeding seems to be continuing through the winter so I doubt I'll have a tank without babies for a while. Would the stress of cleaning and water changes be too much? It would only be for my own benefit so I can watch them more easily.

I don't see any issues cleaning the glass, with it being a sphere id forget cleaning magnets etc and just get some filter floss and grab a ball of it and wipe inside your tank. The algae will cloud the water but it will sink to the substrate after a while and the shrimp will enjoy eating it. Why do you want to change the water? I'm curious

It's a large jar rather than a sphere (yay for picking up old lab equipment) but I have a bottle brush with a long (plastic coated) wire handle that I have used to clean it before. I want to change out the water (maybe 25%) take out some of the nutrient content of the water so that the algae doesn't grow back again as fast. It would be just so I can avoid having to clean it again soon.

I know that the shrimpies hate any agitation of the water and the larvae seem to be the most sensitive to environmental changes, so I wanted to be sure I wouldn't stress them too much and they'd die! I have about 20 larvae and two berried females currently so there are a lot of vulnerable babies (compared to 20 adults in the jar).

Yeah sure change out water if you so wish but make sure when you mix up a batch of fresh brackish water you let the salt dissolve over night at least and let it get to room temperature before adding it in. You can always add a little at a time over a day if you wish.