One of the largest problems with freshwater pisciculture is that it can use a million gallons of water per acre (about 1 m³ of water per m²) each year. Extended water purification systems allow for the reuse (recycling) of local water.

The largest-scale pure fish farms use a system derived (admittedly much refined) from the New Alchemy Institute in the 1970s. Basically, large plastic fish tanks are placed in a greenhouse. A hydroponic bed is placed near, above or between them. When tilapia are raised in the tanks, they are able to eat algae, which naturally grows in the tanks when the tanks are properly fertilized.

The tank water is slowly circulated to the hydroponic beds where the tilapia waste feeds commercial plant crops. Carefully cultured microorganisms in the hydroponic bed convert ammonia to nitrates, and the plants are fertilized by the nitrates and phosphates.

This system, properly tuned, produces more edible protein per unit area than any other. A wide variety of plants can grow well in the hydroponic beds. Most growers concentrate on herbs (e.g. parsley and basil), which command premium prices in small quantities all year long. The most common customers are restaurant wholesalers.

Since the system lives in a greenhouse, it adapts to almost all temperate climates, and may also adapt to tropical climates. The main environmental impact is discharge of water that must be salted to maintain the fishes’ electrolyte balance. Current growers use a variety of proprietary tricks to keep fish healthy, reducing their expenses for salt and waste water discharge permits. Some veterinary authorities speculate that ultraviolet ozone disinfectant systems (widely used for ornamental fish) may play a prominent part in keeping the Tilapia healthy with re-circulated water.