Donald Walker has made important contributions to ecology and palaeoecology, principally of tropical rainforests. His earlier studies first provided a synthesis of late- and post-glacial vegetational history in Cumbria, illuminating the origin and persistence of vegetation differences within a small but diverse region — providing a classic framework for subsequent investigators and illustrating his principal objective of relating ecology and vegetational history. Likewise, his fundamental study of the relation of peat stratigraphy to bog regeneration provided a basis for much subsequent research.

He founded the Department of Biogeography and Geomorphology in the Australian National University. He began pioneering research on the ecology and history of tropical rainforest, first in Papua New Guinea, then in north Australia and southern China, which has led to the revision of widely held views on the stability of tropical rainforests, the timing and magnitude of late-Quaternary climatic change in the tropics, and the age and nature of the impact of human activities. He has also made original applications of statistical methods to the interpretation of palynological data.