To achieve sustainable, healthy closed ecological systems requires solutions to challenges of closing the water cycle – recycling wastewater/irrigation water/soil medium leachate and evaporated water and supplying water of required quality as needed for different needs within the facility. Engineering Biosphere 2, the first multi-biome closed ecological system within a total airtight footprint of 12,700 m2 with a combined volume of 200,000 m3 with a total water capacity of some 6 × 106 L of water was especially challenging because it included human inhabitants, their agricultural and technical systems, as well as five analogue ecosystems ranging from rainforest to desert, freshwater ecologies to saltwater systems like mangrove and mini-ocean coral reef ecosystems. By contrast, the Laboratory Biosphere – a small (40 m3 volume) soil-based plant growth facility with a footprint of 15 m2 – is a very simplified system, but with similar challenges re salinity management and provision of water quality suitable for plant growth. In Biosphere 2, water needs included supplying potable water for people and domestic animals, irrigation water for a wide variety of food crops, and recycling and recovering soil nutrients from wastewater. In the wilderness biomes, providing adequately low salinity freshwater terrestrial ecosystems and maintaining appropriate salinity and pH in aquatic/marine ecosystems were challenges. The largest reservoirs in Biosphere 2 were the ocean/marsh with some 4 × 106 L, soil with 1 to 2 × 106 l, primary storage tank with 0 to 8 × 105 L and storage tanks for condensate and soil leachate collection and mixing tanks with a capacity of 1.6 × 105 L to supply irrigation for farm and wilderness ecosystems. Other reservoirs were far smaller – humidity in the atmosphere (2 × 103 L), streams in the rainforest and savannah, and seasonal pools in the desert were orders of magnitude smaller (8 × 104 L). Key technologies included condensation from humidity in the air handlers and from the glass space frame to produce high quality freshwater, wastewater treatment with constructed wetlands and desalination through reverse osmosis and flash evaporation were key to recycling water with appropriate quality throughout the Biosphere 2 facility. Wastewater from all human uses and the domestic animals in Biosphere 2 was treated and recycled through a series of constructed wetlands, which had hydraulic loading of 0.9–1.1 m3 day−1 (240–290 gal d−1). Plant production in the wetland treatment system produced 1210 kg dry weight of emergent and floating aquatic plant wetland which was used as fodder for the domestic animals while remaining nutrients/water was reused as part of the agricultural irrigation supply. There were pools of water with recycling times of days to weeks and others with far longer cycling times within Biosphere 2. By contrast, the Laboratory Biosphere with a total water reservoir of less than 500 L has far quicker cycling rapidity: for example, atmospheric residence time for water vapor was 5–20 min in the Laboratory Biosphere vs. 1–4 h in Biosphere 2, as compared with 9 days in the Earth’s biosphere. Just as in Biosphere 2, humidity in the Laboratory Biosphere amounts to a very small reservoir of water. The amount of water passing through the air in the course of a 12-h operational day is two orders of magnitude greater than the amount stored in the air. Thus, evaporation and condensation collection are vital parts of the recycle system just as in Biosphere 2. The water cycle and sustainable water recycling in closed ecological systems presents problems requiring further research – such as how to control buildup of salinity in materially closed ecosystems and effective ways to retain nutrients in optimal quantity and useable form for plant growth. These issues are common to all closed ecological systems of whatever size, including planet Earth’s biosphere and are relevant to a global environment facing increasing water shortages while maintaining water quality for human and ecosystem health. Modular biospheres offer a test bed where technical methods of resolving these problems can be tested for feasibility.