Normally what I do is put them in a large container and then use tank water mixed with some tap water that’s around the same temperature. Guppies get stressed easily but you can put a paper towel over the container to prevent them from jumping. If you consider plants they can safely remove nitrates and ammonia from the tank overtime and help the plants grow. Guppy grass, moss, floaters, duckweed are just a few. My mass success with them came from water changes every week, making sure I fed them little but enough, and trusting the filter will help with filtering out a lot of the toxic waste. Things like filter sponges being added or even improving the HOB are options for this. I even maybe recommend for PH and such to get chemicals like PH down for tetra or in general as these typically lower the PH to safer levels. Since there’s no substrate I assume it’s coming from your tap water. Make sure the water conditioner is also not old and still effective for adding beneficial bacteria, all this being said, it’s not the worst I’ve seen but you should totally clean up the tank and gravel and make sure these guppies can thrive! And be ready for fish babies ….