Surface ocean waters generally have oxygen concentrations close to equilibrium with the Earth's atmosphere. In general, colder waters hold more oxygen than warmer waters. As water moves out of the mixed layer into the thermocline, it is exposed to a rain of organic matter from above. Aerobic bacteria feed on this organic matter; oxygen is used as part of the bacterial metabolic process, lowering its concentration within the water. Therefore, the concentration of oxygen in deep water is dependent on the amount of oxygen it had when it was at the surface, minus depletion by deep sea organisms.
The downward flux of organic matter decreases sharply with depth, with 80–90% being consumed in the top .  The deep ocean thus has higher oxygen because rates of oxygen consumption are low compared with the supply of cold, oxygen-rich deep waters from polar regions. In the surface layers, oxygen is supplied by photosynthesis of phytoplankton. Depths in between, however, have higher rates of oxygen consumption and lower rates of advective supply of oxygen-rich waters.  In much of the ocean, mixing processes enable the resupply of oxygen to these waters (see upwelling).
A distribution of the open-ocean oxygen minimum zones is controlled by the large-scale ocean circulation as well as local physical as well as biological processes. For example, wind blowing parallel to the coast causes Ekman transport that upwells nutrients from deep water.  The increased nutrients support phytoplankton blooms, zooplankton grazing, and an overall productive food web at the surface.  The byproducts of these blooms and the subsequent grazing sink in the form of particulate and dissolved nutrients (from phytodetritus, dead organisms, fecal pellets, excretions, shed shells, scales, and other parts).  This "rain" of organic matter (see the biological pump) feeds the microbial loop and may lead to bacterial blooms in water below the euphotic zone due to the influx of nutrients. Since oxygen is not being produced as a byproduct of photosynthesis below the euphotic zone, these microbes use up what oxygen is in the water as they break down the falling organic matter thus creating the lower oxygen conditions.
Physical processes then constrain the mixing and isolate this low oxygen water from outside water. Vertical mixing is constrained due to the separation from the mixed layer by depth. Horizontal mixing is constrained by bathymetry and boundaries formed by interactions with sub-tropical gyres and other major current systems. Low oxygen water may spread (by advection) from under areas of high productivity up to these physical boundaries to create a stagnant pool of water with no direct connection to the ocean surface even though (as in the Eastern Tropical North Pacific) there may be relatively little organic matter falling from the surface.