Carbonate sedimentary rocks in the Fosheim–Hamilton sub-basin at the eastern end of the Sverdrup Basin contain a particularly sensitive record of changing palaeoceanography and faunal turnover during the northward movement of Pangaea through the Late Palaeozoic. Carboniferous and earliest Permian inner ramp carbonates are a photozoan association of colonial corals, fusulinids, algae and ooids, with sparse heterozoan elements (crinoids, brachiopods and bryozoans). Based on modern analogues these biotic components reflect warm-water oligotrophic marine environments. Contemporaneous mid-ramp and basin biotas are dominated by a heterozoan fauna (solitary corals, crinoids, bryozoans and brachiopods) that grew in cooler deeper waters that may have been beneath a thermocline. Initial cooling began in the latest Sakmarian with an influx of cool deep water and climatic deterioration allowing cool and warm waters to mix, disrupting the thermocline, and producing a sub-tropical marine biota whose remains were reworked by storms and re-deposited as tempestites. Faunas are heterozoan (crinoids, bryozoans, brachiopods and sponges) with photozoan elements (colonial corals and symbiont bearing fusulinids) prominent only in inner ramp facies. By late Artinskian these photozoan components are only present in shallowest basin-margin environments. Artinskian subtropical waters contained somewhat elevated trophic resources that together with mixing of photozoan and heterozoan elements in the subtropical inner ramp produced the greatest faunal diversity seen in the Sverdrup Basin. The biota was completely boreal in nature, and warm shallow waters with a warm refuge biota, were now supplemented by cool waters derived from the Panthalassa Ocean. Profound change took place in the Kungurian, coincident with localised uplift during the Melville Disturbance and increased siliciclastic input. Neritic, storm-dominated sediments are wholly heterozoan (brachiopods, bryozoans, crinoids and sponges) with no remaining photozoan elements. Nutrient levels are elevated (but not eutrophic) as indicated by phosphate and glauconite, extensive bioerosion, numerous infaunal foraminifers, and an impressive and diverse shelly biota, that during times of high siliciclastic input was replaced by a profuse Zoophycos infauna. Brachiopod and bryozoan faunas are distinctly boreal. Continued cooling, relatively high nutrients, as indicated by abundant glauconite and phosphate, and decreased siliciclastic input eventually resulted in an abundant heterozoan biota (brachiopods, bryozoans, crinoids and sponges) with local gigantism, but reduced brachiopod and bryozoan diversity. These Middle Permian rocks may be the coolest water deposits in the Sverdrup Basin. The faunas are still part of a boreal Arctic province, with strong ties to cool water faunas of Uralian basin. The succession ends with Late Permian biosiliceous spiculitic cherts containing accessory heterozoan components (brachiopods, bryozoans and few crinoids). These sediments, in part coeval with evaporites and terrestrial red beds on the Eastern European Platform, are interpreted to reflect a combination of cool waters, elevated nutrients, and mid-latitude storminess.