Microorganisms are of major importance in industrial wastewater treatment and aquaculture. They reside in the sediment and other substrates, and in the water of aquaculture facilities, as well as in and on the culture species. Microorganisms may have positive or negative effects on the outcome of aquaculture operations. Positive microbial activities include elimination of toxic materials such as ammonia, nitrite, and hydrogen sulfide, degradation of uneaten feed, and also providing nutrition to aquatic animals such as shrimp, fish etc. These and other functions make microorganisms as key players in the health and sustainability of aquaculture. Yet, microorganisms are among the least known and understood elements in aquaculture. Like other areas in aquaculture, microorganisms require management and manipulation.

The world of microorganisms is made of bacteria, fungi, algae, protozoa, and viruses. They are grouped together only because of their small size, and not by their function. If, for example, the same taxonomical rules were applied to larger animals, some fish, shrimp, green plants, birds and mammals would be grouped together. Some microorganisms such as viruses, bacteria, and protozoa are notoriously small (one mm in diameter). Others, like algae and fungi, have large sized relatives (such as the brown algae that is among the largest living organisms). Unlike larger organisms, the morphology of microorganisms is poorly known, and is confined to a few shapes and colors. However, their poor morphology is compensated by great physiological versatility.

Viruses are very small, ranging between 0.01 and 0.03 microns, and only visible by using an electron microscope. They cannot live independently, and only multiply inside the cells of other organisms. However, their demand for a host is fairly specific. For example, it is unlikely that a crustacean virus will attack humans or fish. Viruses are also the simplest of all organisms and are made of nucleic acid (either DNA or RNA), frequently coated with a protein layer.

Algae are photosynthetic organisms (contain chlorophyll) and obtain their energy from the sun and their carbon from carbon dioxide. Their size ranges from one micron to many meters. All organisms that use carbon dioxide for their carbon requirement are called autotrophs. Algae are generally beneficial in aquaculture by supplying oxygen and as a natural food base for the cultured animals. However, such as dinoflagellates cause red tide when blooms formed.

Fungi are similar to algae, but they do not contain chlorophyll and require pre-formed organic matter as energy and carbon sources (e.g., sugars, fat, protein, and other carbohydrates). Such organisms are called heterotrophs. Fungi, ranging in size from a few microns to several centimeters, grow either independently by feeding on decaying matter, or in association with plants and animals.

Protozoa are heterotrophs, mostly free-living, feeding mainly by devouring smaller microorganisms. Their size ranges between 2 and 200 micron meters. A large group of protozoa, the Sporozoa, are parasites. Small numbers of protozoa contain chlorophyll and can switch over from autotrophic to heterotrophic mode of feeding, based on light conditions.

Bacteria range in size from 0.1 to 15 micron, with some "giants" that may reach half a millimeter. They make up the most metabolically diverse group of living organisms. Although some are parasitic to animals and plants, the majority of bacteria are free-living, having either a neutral or beneficial relationship with humans and other animals and plants. Their metabolic versatility is incredible; while most are heterotrophs, using either light or chemical energy. One of their most remarkable characteristics is their ability to multiply rapidly, with generation times usually ranging between minutes to hours.

Bacteria and other microorganisms, most notably fungi, are able to metabolize and transform numerous organic and inorganic compounds. Therefore, man has used them for thousands of years for making yogurt, pickles, bread, cheese, wine, and more recently for wastewater purification. The Process controlled by microorganisms can occur aerobically or anaerobically. The starting materials and the end products of such processes vary based on the microorganisms' capabilities (as reflected in their genetic makeup), and the environment in which these processes occur (e.g., availability of oxygen, temperature, salinity, pH, etc).

Generally, aerobic microbial processes yield compounds which can be beneficial, and are either not toxic or have low toxicity levels in aquaculture ponds or tanks. Oxidation of organic matter to carbon dioxide is a process that is the main consumer of oxygen in aquaculture ponds or tanks. Oxidation of ammonia to nitrate via nitrite, also consumes large quantity of oxygen, oxidation of reduced sulfur compounds (such as hydrogen sulfide and elemental sulfur) to sulfate, a process that generally has low oxygen demand in aquaculture. Conversion of carbon dioxide to biomass by autotrophic bacteria (such as the nitrifying bacteria) with a relatively small amount of biomass produced in aquaculture facilities, when compared to the conversion of carbon dioxide to biomass by algae.
Conversion of carbon dioxide to biomass by algae depending on the availability of light. Excluding feeding, the photosynthetic process in aquaculture is the main input of carbon source and natural food for aquatic animals.

Microbial anaerobic processes, if not controlled, can produce compounds that are highly toxic to cultured animals. These processes are included: Consumption of organic matter, without the utilization of free oxygen, resulting in products, which are usually not fully oxidized (such as alcohols, organic acids). Reduction of nitrate and nitrite, which can yield either nitrogen gas or ammonia. In aquaculture, due to toxicity of ammonia and nitrite, ammonia production is not welcomed, while nitrogen gas production is beneficial. However, in agriculture, the opposite is true the conversion of nitrate and nitrite to nitrogen has result in a loss of fertilizers. Reduction of sulfur compounds to hydrogen sulfide as a final product, a compound, which is toxic to most animals at even very low concentrations.