This chapter contains an introduction to aquaponics and provides, for instance, technical solutions, species selection, and ways to reduce the operating costs to sustainably grow microalgae and fish in one artificial ecosystem, using the principles of “algaeponics” (combining aquaponics and algae cultivation). Possibilities for high-value products derived from microalgae biomass will be shown, with emphasis on the production of biofuels. To the best of my knowledge, this approach has not been used so far, neither in research nor commercially. Thus, initial experimentation is required to determine, for example, the feasibility for large-scale production of mainly microalgae biomass. Minding the fact that the cultivation of algae for multiple purposes is an expanding industry, algaeponics is a highly promising field to explore, since it has several advantages compared to more common cultivation methods. Promising/recommended technologies for producing biofuel-relevant microalgae using algaeponics are, e.g., recirculating decoupled aquaponic systems, cultivation of algae in open ponds (e.g., raceway type in a greenhouse), and harvesting the biomass by filtration using a semipermeable membrane. A suitable combination of biofuel-relevant microalgae and fish species (based on pH and temperature requirements) is the co-cultivation of the common carp (Cyprinus carpio) and the two green microalgae Chlorella vulgaris and Chlamydomonas reinhardtii to test the production of biofuels (e.g., biodiesel and biohydrogen, respectively). Depending on, for example, the location of the facility (heating vs. cooling of the system water), additional fish/algae combinations can be explored.