The climate warming processes illustrated by Wignall and Twitchett, Siberian trap volcanism and methane hydrate release, are thought to have been the cause of oceanic chemostratification. The melting of high-latitude polar sea ice could have a large impact on global thermohaline circulation. As opposed to cold, dense, saline water sinking in the northern polar region, warmer and fresher melt water would remain at the sea surface, causing stagnation. (Hotinski, 2001) If tropical waters were made to become highly saline and dense via evaporation, would also have dropped to the bottom of the water column. Warm water contains less oxygen than cold water. With warm, saline water in the deep parts of the ocean, the ocean bottom would have become dysoxic. Additionally, in a warmer world, evaporation would be increased. This, in turn, would further raise the salinity of tropical waters. As the density gradient between the tropics and polar regions changed, thermohaline circulation could slow or even change direction. (Horne, 1999)

Oxygen-poor conditions are first recorded from the deep-water, accreted oceanic terranes of Japan in the Late Permian. Such conditions vastly increased in extent in the interval between the latest Permian and the late Griesbachian, when dysaerobic facies are developed in all but the shallowest of marine settings. The Panthalassa Ocean was probably truly euxinic in this interval. Anoxia was never so extensive nor so intense after this interval, and the superanoxic event ceases abruptly in equatorial Tethyan latitudes in the latest Griesbachian. Elsewhere, anoxia persisted at least into the Dienerian Stage in the Perigondwanan shelf sections of Neo-Tethys, and deep-water anoxia may have persisted in Panthalassa until the middle Triassic.

While it is generally accepted by researchers that ocean conditions at the Permian Triassic Boundary were oxygen depleted, there are some sites which confuse this issue.  Bioturbation and deposition under well oxygenated conditions in the Zewan Formation in certain Kashmir beds are one such area. In addition, while beds of the overlying Khunamuh Formation are mostly unbioturbated, suggesting low oxygen conditions, there is an absence of pyrite. A lack of this indicator mineral could mean that the lack of bioturbation in the thinly laminated beds is a result of quick deposition and/or an absence of burrowers, not an absence of oxygen. However, recent reviews of the Kashmir area have revealed that the Perigondwanan margin is anomalous in its having largely escaped benthic oxygen restriction. In a study by Wignall and Twitchett, it is assumed that the laminae of the shallow margins were under low oxygen conditions, but the deeper areas were anoxic during the Permian-Triassic Boundary. (Wignall and Twitchett, 2002)