El Niño, as well as all other causes of climate fluctuation has been recorded throughout time in the geological record by such organisms as coral, the varved sediments left by oceanographic upwelling, tree rings as well as other related indicators. Also, reports of severe and prolonged desert flooding, massive crop failures, disease and insect infestations, as well as marine observations from ships logs have provided a good index to the occurrences of El Niño's past episodes.

(Taken from www.cdc.noaa.gov)