substrate question

i believe you can, it is just a very delacate process,
 
what are you trying to change to? if its gravel to sand i wouldnt leave em in there as the sand blowing around could irritate their gills, not to mention what its gonna do to your filters impeller
 
I would probably err on the side of caution, and remove the fish regardless of what you're changing it to. It'll be easier all around.

What I would do, assuming you have gravel currently, and depending on the types of fish, get a rubbermaid bin or other large container, move some tank water to that, add your fish to it, put your filter on there as well and turn it on to help preserve the beneficial bacteria(assuming this is going to be rather time consuming as well from my own experiences.....). Do a really good gravel vacuum of the substrate, and drain the water down at least half way as well. Remove your substrate, then add your new substrate. Refill with some new water, let everything settle for a bit(especially important if you're using sand), then turn your filter on. Let it run a bit, then start adding a bit of water to the container holding the fish so they can adjust in case of any temperature or ph changes. Have fun I don't envy you :)
 
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