The Habitat for Atlantis 1 will have internal systems for air, water, waste, power, heating, cooling, and the transportation of supplies. All of these devices will be automatically controlled to ensure the health and safety of the participants aboard Atlantis 1. These systems will also have an in/out valve (to replenish, i.e. air; or empty, i.e. wastes) in the bottom floor-"Shira Floor" attached to the device itself (stored on the top floor-"Alex Floor").

The air will be composed of a solution of helium, oxygen, nitrogen, and other gasses. Each type of air will be stored in its own tank and mixed together (in its appropriate concentrations) when needed. For a depth of 41.6 meters below sea level (the bottom of the habitat when placed in the blue hole) the gasses will need to be in the following concentrations: oxygen 4.0%, nitrogen 26.7 %, helium 69.1 %, other 0.19 %. Therefore, the volume of gasses required to keep 9 people alive for 16 days (two days longer than the average mission) are as follows: 494,000 liters of oxygen, 3,293,000 liters of nitrogen, 8,523,000 liters of helium, and 23,000 liters of other gasses. To ventilate the air there will be two sets of vents going vertically along opposite sides of the habitat. One side of the vents will be for air flowing into the room and the other will be for air flowing out of the room. Each vent will have the ability to (automatically or manually) close in the case of an emergency. The top-"Alex floor" and bottom floors-"Shira Floor" will only have an in/out section, but the second floor-"Calvin Floor" will have branched sections, which will go into the lab to supply it's own source of air. On the top floor-"Alex Floor", the air will pass through a filter surrounded by water pipes, which will heat or cool the habitat as necessary.

Clean water and waste will traverse the habitat on one side of the habitat (next to the vents of filtered air). There will be three pipes, hot water, cold water, and wastewater. Some water will travel past the habitat's power source to increase the waters' temperature (creating hot water) and some will travel through a refrigerant to supply the habitat with cold water. The wastewater will pass through a water filtration unit, which will clean the water and trap the waste. The water will then be re-introduced to the habitat's water system.

Hydrogen fuel cells will generate the power needed to run the Atlantis 1 habitat. The 200 KW hydrogen fuel cells will be stored in the top floor-"Alex Floor" of the habitat, with two pipes leading away from it down to the bottom floor (used to refill hydrogen and oxygen supplies). Hydrogen fuel cells generally weigh 1 kg per kW produced, thus this device will have a mass of about 250-300 Kg (including more protection for pressure). The reaction will require a 2 to 1 molar ratio between hydrogen and oxygen. To counteract the heat generated by the fuel cell (about a 0.04 degree change in temperature when applied throughout the entire habitat), seawater will pass around the fuel cell (via a pump) and draw off the heat-and ejected back into the water.

The pipes of seawater will also pass/surround the air vents on the top floor-"Alex Floor". Depending on the direction of water flow, the air will heat up or cool down to a desired temperature. If the water flows past the vents, and then the fuel cell, the air within the habitat will cool off. If you reverse the water's direction, it will flow past the fuel cell and then the air vents, warming the air. Both the hydrogen and oxygen required to run the fuel cell will be in containers, and stored at the top of the habitat. The water exhaust will flow into the drinking water, stored for electrolysis (to be used in the reaction), emitted into the environment, or stored and brought back to the surface. The determination of the exact model of hydrogen fuel cell will give an answer to what happens to the exhaust. (For example the use of a discrete regenerative fuel cell, it will break up the water exhaust and form hydrogen and oxygen again to generate more electricity)

A typical excursion will last about fourteen days (thus all supplies will be made to withstand at least sixteen days). The habitat optimally holds six people, however it can hold up to nine people. Aboard a ship, above the habitat, the researchers will pressurize themselves (in a compression chamber) to the depth of just over five atmospheres and travel down to the habitat via a transport vehicle. The transport vehicle will enter the already pressurized habitat through the moon pool on the bottom floor. From there, they will be able to exit the vehicle, enter the habitat, and begin working. The manned robotics vehicles will attach to the habitat via the hatch on the top floor-"Alex Floor" of the habitat. All pipes necessary to refill/empty their respective containers will be within reach of the transport vehicle, so that no one has to carry containers to and from the top of the habitat.

The above steps are necessary because of the moon pool on the bottom of the habitat. The moon pool will (for the most part) remain open. To prevent water from entering the habitat, the air pressure must equal that of the water pressure outside the habitat at the moon pool. In addition, the habitat must stay at the same pressure so that it does not disturb/break lab equipment (due to changes in pressure). Therefore, the researchers must pressurize themselves to the fixed pressure of the habitat rather than the habitat adjusting its pressure.