I am so sorry to hear your little guy is having problems.
How big is this Pleco?
Are you familiar with the nitrification cycle?
This is a good article which has a bunch of important care information.
https://www.aquariumadvice.com/guide-to-starting-a-freshwater-aquarium/
Your tank needs to have beneficial bacteria / BB in it to process waste.
When you throw out the filter pads or wash them in plain tap water with chlorine (kills bacteria to make water okay to drink), you throw out a large amount of or kill off BB that is in the tank. When you change the substrate you are throwing out the BB which has colonized there as well.
What other fish are in the tank?
What are you feeding the Pleco?
What is the temperature and do you know your water parameters?
Getting the water freshened up will be a big help.
When was the last pwc? Try doing a couple of 40-50% pwc (back to back /one after the other) if you have done a pwc in the last week. Temperature matched and dechlorinated correctly (in case your town has chloramines it is double dose if your dechlorinator neutralizes chloramines).
Back to back helps ease the water quality difference from old water to fresh clean water, making the change less more gentle for the ill fish.
If you can check the water quality please do and write it down to compare. If you have to take it to the store for checking please grab a cup /sample before you start.
If you have changed the filter pads and substrate then you are basically going through a fish-in cycle.
https://www.aquariumadvice.com/i-just-learned-about-cycling-but-i-already-have-fish-what-now/
https://www.aquariumadvice.com/fishin-cycling-step-dark-side/
Get a freshwater master test kit online is often a good deal. But the big box pet stores will usually price match if the item is from their own online better price, or the petco, petsmart or Chewy, sometimes Liveaquaria. They can be particular. So you might want to call and check as its a $25-ish item. (just checked and it is $23.22)
Also some have a buy online and save 10% when picking up in store.
If, your after water change samples are still unsafe, do one or another back to back water change.
*** Or if you haven't done a pwc in the past week, then start doing the same process but with a smaller amount of pwc like 25% back to back. Then wait a few hours and do another 2 pwc back to back.
Again this is to make the changes in water easier for your ill fish to deal with it.
Keep up the pwc's until the water is safe. Limit feeding to a minimum and make sure there isn't a bunch of food to waste.
Read the articles.
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The next part will be medication probably needed. But fish can heal with a series of daily pwc to keep water perfect, so he isn't further stressed.