Aquaculture production systems may range from tanks and raceways, in which water quality is controlled by water dilution and discharge to the environment to captive water systems, in which water quality is controlled by microbial reactions within the tank or pond. Attempts at intensification of pond aquaculture beyond the commonplace practice of supplemental aeration may be classified into categories of physical/chemical techniques and a broad range of microbial techniques. Most of these techniques are directed at raising the ‘ceiling’ of the system ammonia detoxification rate. Physical–chemical techniques for intensification of pond aquaculture have included use of in-pond cages and raceways, water blending and shading of the algal community, as well as, direct flocculation and removal of algal and bacteria biomass from ponds. A variety of microbial processes can be used to reduce ammonia levels in a conventional pond. These processes include nitrification/denitrification, photosynthesis, and heterotrophic bacterial re-growth. In this paper, simplified microbial growth fundamentals, and elemental mass balances are used to analyze and compare the various aquaculture intensification techniques and, in particular, to compare conventional and heterotrophic techniques to the use of high rate photosynthetic systems. Direct or indirect photosynthetic systems include enhanced algal systems (with water mixing), polyculture, hydroponics, wetlands, and terrestrial irrigation/fertilization. The development of Clemson University's Partitioned Aquaculture System (PAS) constitutes an attempt to combine a number of the various physical, chemical, and microbial intensification techniques into a single integrated system. The PAS represents an adaptation of high rate microalgal culture to produce a sustainable, minimal discharge, high yield, and more controllable fish production process. The PAS combines the advantages of process control of recirculating tank aquaculture with the lower costs of earthen pond aquaculture. Central to the economic success of the PAS is the use of low speed (1–3 r.p.m.) paddlewheels as an energy efficient means of establishing a uniform water velocity field within an aquaculture pond. The PAS represents a redesign of the conventional aquaculture pond culture technology providing a spectrum of applications ranging from moderate yield (6700–11 200 kg/ha) ‘engineered ecosystems’ to high yield (16 800–33 600 kg/ha) controlled ‘production processes’. This high rate photosynthetic system offers the potential for a 90% reduction in total water usage per unit of fish produced. The modular nature of the PAS, the increased productivity per unit area, reduced water requirement, and reduced environmental impact offers the potential for fish culture systems to be installed at sites not currently suitable for conventional aquaculture.