Historical ecology is a research program that focuses on the interactions between humans and their environment over long-term periods of time, typically over the course of centuries. In order to carry out this work, historical ecologists synthesize long-series data collected by practitioners in diverse fields. Rather than concentrating on one specific event, historical ecology aims to study and understand this interaction across both time and space in order to gain a full understanding of its cumulative effects. Through this interplay, humans both adapt to and shape the environment, continuously contributing to landscape transformation. Historical ecologists recognize that humans have had world-wide influences, impact landscape in dissimilar ways which increase or decrease species diversity, and that a holistic perspective is critical to be able to understand that system.

Piecing together landscapes requires a sometimes difficult union between natural and social sciences, close attention to geographic and temporal scales, a knowledge of the range of human ecological complexity, and the presentation of findings in a way that is useful to researchers in many fields. Those tasks require theory and methods drawn from geography, biology, ecology, history, sociology, anthropology, and other disciplines. Common methods include historical research, climatological reconstructions, plant and animal surveys, archaeological excavations, ethnographic interviews, and landscape reconstructions.

The discipline has several sites of origins by researchers who shared a common interest in the problem of ecology and history, but with a diversity of approaches. Edward Smith Deevey, Jr. used the term in the 1960s to describe a methodology that had been in long development. Deevey wished to bring together the practices of "general ecology" which was studied in an experimental laboratory, with a "historical ecology" which relied on evidence collected through fieldwork. For example, Deevey used radiocarbon dating to reconcile biologists’ successions of plants and animals with the sequences of material culture and sites discovered by archaeologists.

In the 1980s, members of the history department at the University of Arkansas at Little Rock organized a lecture series entitled "Historical Ecology: Essays on Environment and Social Change" The authors noted the public's concerns with pollution and dwindling natural resources, and they began a dialogue between researchers with specialties which spanned the social sciences. The papers highlighted the importance of understanding social and political structures, personal identities, perceptions of nature, and the multiplicity of solutions for environmental problems.

The emergence of historical ecology as a coherent discipline was driven by a number of long-term research projects in historical ecology of tropical, temperate and arctic environments:

E.S. Deevey's Historical Ecology of the Maya Project (1973-1984) was carried out by archaeologists and biologists who combined data from lake sediments, settlement patterns, and material from excavations in the central Petén District of Guatemala to refute the hypotheses that a collapse of Mayan urban areas was instigated by faltering food production.

Carole L. Crumley's Burgundian Landscape Project (1974–present) is carried out by a multidisciplinary research team aimed at identifying the multiple factors which have contributed to the long-term durability of the agricultural economy of Burgundy, France.

Thomas H. McGovern's Inuit-Norse Project (1976–present) uses archaeology, environmental reconstruction, and textual analysis to examine the changing ecology of Nordic colonizers and indigenous peoples in Greenland, Iceland, Faeroes, and Shetland.