First off, if your nitrates are running high, you don't have a large enough bio-filter to sufficientently handle the amout of nitrites produce by the fish and this will cause them stress and the weakest die first.

Secondly, if you have sufficient bio_filter power, there is never a need for a water change. When you remove water from the system and replace it with water from elsewhere, you knock the whole system completely out of balance. In Aquaponics, you are only suppose to add water to replace for evaporation and that used by the plants.

An oversized bio-filter and plenty of oxygenatioin are the keys to a healthy Aquaponic system Take care of that and then step back and keep you fingers out of the soup.