Oxygen, which is determined by flow, if any, algae bloom (which adds oxygen by day and depletes it at night or in cloudy weather), nitrite/nitrogen buildup, pathogens and toxic pond muds from buildup of organic material. Fallowing, or drying the pond in a regular cycle is important to control pathogens and toxic pond bottom.

What sets the limits of farmed fish production in a closed water body are as follows:

1. Feed quality and right feeding protocol

2. Proper management

3. Water quality

4. The stocking density

Broadly speaking, carrying capacity in a closed system will be determined by the system's 'ability' (natural and/or man-made) to provide dissolved oxygen (DO) in the required concentration and to remove toxic waste products notably ammonia-N, ammonia, nitrite, and hydrogen sulphide. In the presence of high levels of oxygen higher levels of waste products can be tolerated. pH and salinity will have their effects as each cultured species will have a range where it is most comfortable. If the system is a greenwater pond the balance between daytime and nighttime DO will need to be carefully managed - thick algal blooms in the day that provide high DO levels can be disastrous at night when the production of CO2 begins. There will be a finite stocking density that should not be exceeded. Unused feed applied to the closed system will have its own oxygen demand thus feed rates must be considered.

monitor, DO,  PH, Ammonia, Temp, nitrates..basically, maintain 5ppm or above,  PH at 6-8, 1ppm or less, Temp for specific species,  1ppm or less respectively.

For intensive production in fed ponds, nutrient loads are limiting.  The amount of respiration affects night time oxygen levels.  Phytoplankton and zooplankton have the greatest impact on respiration in ponds (roughly 4 times greater than that of fish).  Nutrient loads stimulate growth of plankton biomass.  Nutrient loads are directly related to the amount of feed fed.  A standard U.S. catfish production recommendation is that 1.0 hp of mechanical aeration should be available for each 22 lb of feed/acre (4 acre-feet) fed per day for intensive aquaculture.

Balanced nutrition on the basis of species specific nutrients requirement can enhanced fish production in captivity, which ultimately limit the nitrogen loads virtually controlled pollution level in pond. 

If I recall correctly, channel catfish only use 30-40% of dietary protein content.  The remainder is used for energy and the nitrogen is excreted as ammonia.  Catfish feed formulations have been well researched and refined.

Thanks

Limitations of farmed fish production in a closed water body besides suitable site and species selections are: carrying capacity, manuring and fertilisation of the ponds, nutritional requirements, physico-chemical parameters, health conditions and managerial practices.