In intensive aquaculture systems, ammonia-nitrogen buildup from the metabolism of feed is usually the limiting factor after dissolved oxygen to increasing production levels. Currently, large fixed-cell bioreactors are the primary strategy for controlling inorganic nitrogen in intensive recirculating systems. This option utilizes chemosynthetic autotrophic bacteria, Ammonia Oxidizing Bacteria (AOB) and Nitrite Oxidizing Bacteria (NOB), for the nitrification of ammonia-nitrogen to nitritenitrogen and finally to nitrate-nitrogen. In the past several years, zero-exchange management systems have been developed based on heterotrophic bacteria and promoted for the intensive production of marine shrimp and tilapia. In these systems, heterotrophic bacterial growth is stimulated through the addition of carbonaceous substrate. At high carbon to nitrogen (C/N) feed ratios, heterotrophic bacteria assimilate ammonia-nitrogen directly from the water replacing the need for an external fixed film biofilter. Thus in these types of systems, build-up of suspended solids may become the second limiting factor after dissolved oxygen. This presentation reviews the two nitrogen conversion pathways used for the removal of ammonia-nitrogen in aquaculture systems, autotrophic bacterial conversion of ammonia-nitrogen to nitrate nitrogen, and heterotrophic bacterial conversion of ammonia-nitrogen directly to microbial biomass. The first part reviews in detail the two ammonia removal pathways, presents a set of stoichiometric balanced relationships, and discusses their impact on water quality. In addition, microbial growth energetics are used to characterize production of volatile and total suspended solids for autotrophic and heterotrophic systems. A critical finding of this work was that only a small fraction of the feed’s carbon content is readily available to the heterotrophic bacteria. For example, feed containing 35% protein has only 109 g/kg feed of labile carbon. In the second part, the results of a study on the impact C/N ratio on water quality. In this experimental trial, sufficient carbon in the form of sucrose (sugar) was added daily at 0%, 50% and 100% of the feed rate to three proto-type zero-exchange systems. The system was stocked with marine shrimp (L. vannamei) at modest density (150 /m2) and water quality measured daily. Significant differences were seen between the three systems in the key water quality parameters of ammonia-nitrogen, nitrite-nitrogen, nitrate-nitrogen, pH and alkalinity. The control system exhibited water quality characteristics of a mixed autotrophic/heterotrophic system and the two systems receiving supplemental carbon, water quality characteristics of pure heterotrophic systems.