Fish produce waste all the time in their urine and poo and from their gills, it is broken down into ammonia which is toxic to fish and if in high levels can burn or kill the fish.
In the filter there is beneficial bacteria that eat this ammonia and turn it into non toxic substances, and if you dont have good enough filtration (goldfish arevery messy and produce a lot of ammonia) there wont be enough bacteria and you will have ammonia present in your water.
I advise getting some test kits to test for ammonia, nitrites (also toxic) and nitrates (safe in low numbers, below 20ppm is good).
Could you answer how many fish in what size tank please? it would help a lot.