It seems that in some water districts they are using chloramines instead of chlorine to disinfect the water that comes out the tap. This is a big problem for anyone with fish because chloramines are toxic to fish, and are quite difficult to remove from the water.
To test for chloramines you will need two tests. Get a basic ammonia test and a chlorine test that tests for either total chlorine or combined chlorine (not free chlorine). If the water test positive for both chlorine and ammonia then your water district is using chloramines.
To remove the chloramines you have a few options. You can boil the water, but that would likely be too expensive for an aquaponic system. You can also degas the water, but it may take a fairly long time (months) before it will test negative. Sodium thiosulphate is likely the best solution because it will quickly neutralize the chloramines. Dissolve 7 parts pure sodium thiosulphate for each part chloramine into a small amount of water, then add to the full body of water you are treating. The water should test negative for chlorine when finished.
Once the chloramines have been removed, you do still have a quantity of ammonia in the water which could cause an ammonia spike if you add too much water too quickly to a working system (it will cause a spike if the system is not yet cycled). Simply add the water such that the bacteria in the system are given enough time to convert the ammonia into nitrates that the plants can consume. How quickly you add water will depend on the amount of ammonia, the quantity of water already in the system, the availability of bacteria, and how many plants you have to take up the new nitrates.
You can poison the fish with too many nitrates, but it does take quite a lot before the fish will start to be adversely affected. Note that you should never drink the aquaponic water if nitrates are detected since they are poisonous to humans in much smaller quantities than in fish.