Here is a list of documents relating to water quality issues in aquaculture. 

Algae Blooms in Commercial Fish Production Ponds

Ammonia in Fish Ponds

Bugs

Carbon Dioxide in Fish Ponds

Controlling Clay Turbidity

Cost of Alternative Effluent Treatments for Catfish Production

Fertilization of Fish Fry Ponds

Interactions of pH, Carbon Dioxide, Alkalinity and Hardness in Fish Ponds

Management of Effluent From Fish Ponds

Managing Ammonia in Fish Ponds

Measuring Dissolved Oxygen Concentration

Nitrite in Fish Ponds

Pond Mixing

StonyPoster (creatures that indicate water quality)

Toxicities of Agricultural Pesticides

Water Quantity and Quality Requirements