Numerical climate models as well as carbon isotope measurements from preserved Ordovician soils suggest that atmospheric levels of carbon dioxide during the period were 14–16 times higher than today. These high levels were driven by widespread volcanic activity, which would have released large volumes of carbon dioxide into the atmosphere. The extensive flooding of continents due to high sea levels, combined with the lack of widespread vegetation on land, would have suppressed the weathering of silicate rocks, a major mechanism for removing carbon dioxide from the atmosphere. In short, the rate at which carbon dioxide was added to the atmosphere increased during the Ordovician Period, whereas its rate of removal decreased.

Because of the greenhouse effect, high levels of atmospheric carbon dioxide would have caused temperatures to rise everywhere from the Equator to the poles. Clear evidence of warm temperatures in the tropics can be seen in the extensive Ordovician limestone deposits with features similar to those found in modern tropical carbonate areas, such as the coral reefs of the Bahamas. Other evidence suggesting warm low-latitude climates in the Ordovician include bauxite deposits in Kazakhstan and evaporite minerals in North America, Australia, China, Kazakhstan, and Siberia.

Warm tropical regions would have fostered the development of tropical cyclones; there is a rich record of such storms in the Ordovician. In subtropical areas of North America, sedimentary deposits from Ordovician continental shelves commonly occur in alternating beds of shale and either sandstone or limestone. These sandstone and limestone beds display evidence of erosion at their bases, become finer-grained upward within the beds, and contain distinctive sedimentary structures known to form from the combination of strong currents and large waves. These storm-driven structures and processes also occur on the continental shelves of the present day. In addition, storm deposits known as tempestites can be quite common in Ordovician rocks. For example, an interval of Late Ordovician strata near Cincinnati, Ohio, is 65 metres (213 feet) thick. This interval represents an estimated 1.5 million years of deposition and contains over 300 tempestites. Because the erosion of the seafloor during the early phases of a hurricane has the potential to remove previously deposited tempestites, the interval near Cincinnati suggests that storms left a preserved sedimentary record at least once every 5,000 years during the period.

Despite high carbon dioxide levels in the Ordovician Period, evidence of cooler climates in higher latitudes is seen by the presence of unweathered mica in sedimentary rocks from North Africa, central and southern Europe, and much of South America. Their abundance, coupled with the presence of faunas interpreted as cold-water forms, as well as paleomagnetic evidence, suggests that northwestern Africa was located over the South Pole. Furthermore, glacial deposits dating back to the Ordovician are also known from much of Africa, southern Asia, and parts of Europe. It had been thought the South Pole was glaciated for much of the Ordovician, but more-recent dating of these glacial deposits, plus isotopic evidence, suggests that major continental glaciation was limited to the last half-million years of the Late Ordovician Epoch and a shorter portion of the Early Silurian Epoch.

However, evidence of heavier oxygen isotopes and falling sea levels suggests that continental glaciation could have occurred as early as the Middle Ordovician. The resulting temperature gradient in the oceans likely enhanced the strength of major currents and the upwelling of nutrients from the ocean’s depths (see also marine ecosystem: biological productivity). Some scientists argue that these changes could have created new nutrient-rich habitats that accelerated the rate of speciation during the Ordovician.

How continental glaciation could have formed when carbon dioxide levels were so high has been a paradox. Recently it has been proposed that the terminal Ordovician glaciation was triggered through a combination of the placement of Africa over the South Pole and a short-lived drawdown of atmospheric carbon dioxide. This drawdown was favoured by declining volcanism during the Ordovician, which would have introduced progressively less carbon dioxide into the atmosphere. Increasing orogeny and uplift during later Ordovician times would have accelerated the removal of carbon dioxide from the atmosphere through the weathering of silicate rocks. Once snow began to accumulate in North Africa, the increased albedo (surface reflectance) of the snow would have fostered lower temperatures and increased the accumulation of greater amounts of snow in Gondwana, thereby bringing about a glacial period. The cooling of the oceans may also have fostered the increased productivity of photosynthetic organisms, moving nutrients from the depths to the surface through the process of upwelling. As the populations of photosynthesizers increased, additional carbon dioxide was removed from the atmosphere. At the end of this glacial period, it is now believed, as the production of carbon dioxide from volcanoes continued, the proportion of atmospheric carbon dioxide removal due to the weathering of silicate rocks declined. The silicate rocks of Gondwana had no access to the atmosphere, because many were covered by thick layers of glacial ice.

Marine organisms

Microfossils and plankton

Ordovician seas were characterized by a rich and diverse assemblage of species. Calcified microbial mats, known as stromatolites, are found in Ordovician rocks, although they are not as common there as in strata from the Proterozoic Eon and Cambrian Period (2.5 billion to 485.4 million years ago). Chitinozoans or acritarchs, microfossils with a hollow cavity and organic walls, represent the phytoplankton (small, free-floating, photosynthetic organisms). Ordovician foraminiferans include both agglutinated (glued or cemented) and calcareous (containing calcium carbonate) forms, including the first fusulinids (single-celled, amoeba-like organisms with complex shells). The siliceous radiolarians (spherically symmetrical organisms with fine, sculptured skeletons) that lived as zooplankton (groups of small animals that feed on phytoplankton) are also found in Ordovician rocks.