The archaeological record for natural disasters is a long one, as you might imagine. Over the last 20,000 years, human societies have risen and fallen like the tides. The reasons for the rise of such societies are multiple, as are the reasons for their destruction: attacks from the outside, revolution from the inside, pollution or depletion of necessary resources.
These are cultural factors at work, the effects of humans. Ongoing climatic fluctuations are always troubling, such as the El Niño Southern Oscillation (ENSO), the current of warm water in the Pacific ocean which plays havoc with the weather of the world. ENSO has been impacting the archaeological sites of Peru for at least the past 1,200 years: Inca architecture is thought to have been developed against the ravages of el Nino storms.
But in addition, all societies were and are subject to natural disasters or, as the insurance people would like to say "acts of god."
Here are a few of the historic and prehistoric natural disasters that are known to archaeologists.
Mount Toba Erupts: ~74,000 BP
The effects of the Mount Toba (Sumatra) eruption are debated, but there is no doubt that it was a monster. It involved a minimum of 2,800 cubic kilometers (~670 cubic miles) of magma, and 800 km3 of volcanic ash and gases were injected into the atmosphere. Mount Toba's ashes covered all of Sumatra and ash plumes covered an area from the South China Sea to the Arabian sea: some scholars believe it was this eruption that wiped out our species in Eurasia.
Santorini Volcano Erupts: 1500 BC
About 1500 BC, an earthquake shook the the Minoan civilization city of Akrotiri, on the tip of the active volcano called Thera or Santorini. Subsequently, years and possibly decades later, the volcano erupted, burying the site under meters of volcanic debris.
Some archaeologists postulate this enormous eruption as one reason for the end of the Minoan culture, although the dates don't seem to match. There was apparently ample warning this time; no human remains were found in Akrotiri, and in fact the eruption protected and preserved several stunning wall frescoes.
The explosive end of Akrotiri has been suggested as one of the possible sources for the legend of Atlantis.
Mediterranean Earthquake: 1250 BC
Between about 1300 and 1200 BC, an earthquake hit the Mediterranean, causing damage to the Cretan and Greek palaces of the Mycenaean culture and Troy. Some researchers are of the opinion that the "Trojan Horse" of Homer's the Iliad was a metaphor for the earthquake, which damaged the fortification walls of the cities and made invasion easier.
Xitle Erupts: 50 BC
About 50 BC, the volcano Xitle erupted, covering the city of Cuicuilco, Mexico. Cuicuilco was a large and impressive settlement in the Basin of Mexico, with a population of perhaps 20,000. When Xitle erupted, lava covered 80 square kilometers of the town and region to depths of up to 10 meters (~33 feet). The pyramid at Cuicuilco, a circular stepped pyramid nearly 20 meters high and 110 meters across, was hidden from sight until the 1920s.
Vesuvius Erupts: AD 79
The most famous historic eruption is of course, that of Vesuvius in 79 AD, which destroyed Herculaneum and Pompeii, killed thousands of people. Because it came without much warning, the cities were preserved under ashfall, providing us with a nearly complete picture of life in Roman towns in Italy in the first century AD.
Loma Caldera Volcano Erupts: AD 595
One early evening in August, the people in the town of Cerén in El Salvador were just sitting down to dinner when the Loma Caldera volcano erupted, sending a fiery mass of ash and debris up to five meters thick for a distance of three kilometers. Like Vesuvius, the Loma Caldera preserved many of the tiny details of life as it was lived in central America 1,400 years ago.
Earthquake in the Caribbean: 1672
On June 7, 1692, at 11:43 am, a total of 33 acres of the "wickedest city on earth," Port Royal, Jamaica, was dropped into Kingston Harbor by a massive earthquake. Port Royal was a haven for pirates preying on the English trade vessels, including the pirate/privateer Henry Morgan. The effects of the earthquake dropped many buildings right into the sea. Perhaps 2000 residents were killed that day, many others died in the following days and weeks.
Tsunami in Pacific: 1700
On January 26, 1700, at 9:00 am local time, an enormous tsunami washed over the coasts of Japan, with waves ranging in height from 2-3 m (4-6 feet). Such a tidal wave could only have resulted from an enormous earthquake somewhere on the eastern shore of the Pacific Ocean. Researchers at the University of Washington have used computer models to identify probable locations, and found geological evidence of a +9 magnitude earthquake--and the resulting tsunami--from Cascadia in the American states of Washington and Oregon.
Corroborating evidence for the earthquake and tsunami were recovered from an archaeological site on the Salmon River in Oregon, radiocarbon dated between 1695-1710. Part of a Makah village called Ozette was overrun by mudslides caused by this earthquake. Six houses were sealed under the mud, preserving basketry, wood and cloth, revealed when it was excavated in the 1960s.
Mount Tarawera Erupts: 1886
June 10, 1886, Mount Tarawera, New Zealand, erupted, spewing rocks, ash and boiling hot mud over the village of Te Wairoa, killing 150 people. Te Wairoa was a historic period town, and a tourist location for the Pink and White Terraces, a mineral spring site popular among tourists until they were destroyed by the eruption.
Clarkson C, Jones S, and Harris C. 2012. Continuity and change in the lithic industries of the Jurreru Valley, India, before and after the Toba eruption. Quaternary International 258(0):165-179.
Cordova F. de. A. C, Martin del Pozzo AL, and Camacho JL. 1994. Palaeolandforms and volcanic impact on the environment of prehistoric Cuicuilco, southern Mexico City. Journal of Archaeological Science 21:585-596.
Elson MD, Ort MH, Hesse J, and Duffield WA. 2002. Lava, Corn, and Ritual in the Northern Southwest. American Antiquity 67(1):119-136.
Losey RJ. 2005. Earthquakes and tsunami as elements of environmental disturbance on the Northwest Coast of North America. Journal of Anthropological Archaeology 24(2):110-116.
Manning SW, Bronk Ramsey C, Kutschera W, Higham T, Kromer B, Steier P, and Wild EM. 2006. Chronology for the Aegean Late Bronze Age 1700–1400 B.C. Science 312(5773):565-569.
Martin Del Pozzo AL, Córdoba C, and López J. 1997. Volcanic impact on the southern Basin of Mexico during the Holocene. Quaternary International 43–44:181-190.
Minor R, and Grant WC. 1996. Earth-quake induced subsidence and reburial of Late Holocene archaeological sites, northern Oregon coast. American Antiquity 61(4):722-781.
Sheets PD, and McKee BR. 1994. Archaeology, Volcanism, and Remote Sensing in the Arenal Region, Costa Rica. Austin: University of Texas Press.