The farming of aquatic organisms is called Aquaculture. Fish and algae farming could be beneficial to a settlement. Aquaculture is more resource intensive than plant-based agriculture, but is often more efficient than growing terrestrial animals, especially as part of a wastewater and biomass recycling program.
Single celled algae (microalgae) is grown in tanks of aerated (with carbon dioxide), nutrient rich water. Waste biomass and wastewater can be used as a nutrient source, as long as they are free of toxic chemicals. When the algae has reached the desired population density, the water is filtered, and the algae removed for processing.
Greenhouses or photobioreactors are a good locations for microalgae, due to the abundant light and reasonable temperature ranges. Chlorella vulgaris and Spirulina (Arthrospira platensis, etc) have been proposed as promising species to grow for food.
As long as clean water and food is continually cycled, many sedentary species of mollusk can be grown at a relatively high population density. Commonly farmed mollusks include geoducks, abalones, and clams.
The various forms of aquaculture may be integrated with each other, or even with aquatic or hydroponic plants. Even herbivorous fish may be grown in tanks with plants and macroalgae, as long as they are separated by nets or screens.