The fossil record contains a history of the evolution of life on Earth and provides geologists with a chronology far more detailed and widely applicable than that of geochemistry. It also contains much information about the geographical-ecological changes that have occurred in the course of geologic time. This interpretation of the fossil record predates the other, in that some of the early Greek philosophers and Renaissance naturalists recognized certain strata as marine and as evidence of former higher sea levels, on the basis of the enclosed fossils, long before the evolutionary nature of fossils was known.

The best example of this is the recognition of ancient seas and landmasses. The deposit of loess containing grass seeds and land-snail shells can be quite easily recognized as the windblown accumulation of dust in an ancient grassland or prairie. The accumulation of peat or coal, containing abundant woody material along with spores or pollen, and possibly skeletons of land animals, is evidence of an ancient peat bog or swamp. A bed of limestone containing a wide variety of clams and snails belonging to marine families, as well as the remains of sea urchins or other echinoderms (a phylum that seems always to have been restricted to the sea), is evidently of marine derivation.

The fossil record can be used to reconstruct ancient environments. For example, strata of Tertiary age in the oil-bearing "transverse basins" of California, such as the Los Angeles and Ventura basins, contain many microfossils of the protozoan group called foraminifera. These were studied because they provided a means of tracing strata from one oil well to another, in accumulations of sediment thousands of meters thick. This sedimentary sequence began with stream deposits in the Oligocene epoch, passed through a long marine phase in the Miocene and Pliocene, and reverted to mammal-bearing alluvial deposits in the Pleistocene Epoch. In order to learn something about the conditions under which the oil-bearing marine portion was deposited, paleontologists compared the fossil assemblages with the depth range of the same species or the most closely related species living today off the California coast. Interpreted in this manner, environmental change from continental, through shallow near-shore, into deep-water (more than 1,500 m/5,000 ft), back through the shallow water, and into alluvial was revealed. This history has been confirmed by the study of fossil fish scales. Although sardine scales are found throughout the marine parts, angler fish and other species of the bathyal zone are found only in association with deep-water foraminifera.

This is one example of the field of study that is called paleoecology. Palynologists studying pollen grain assemblages from lake beds and peat bogs have determined the shifting of forests and grasslands that occurred in the later stages of the Pleistocene ice age and in the interval since then and are establishing a much-needed history of climates, which can be related directly to the historical record. Study of the foraminifera in marine cores enables ocean currents and water masses during the height of the last glaciation, 18,000 years ago, in an effort to understand that ice age and its cause.

Fossil chemistry is another area of research for paleoecologists. Many elements occur in two or more atomic forms that differ from each other in weight - isotopes. Thus, oxygen occurs as O16 and O18, O16 being by far the most abundant. When an organism such as a foraminifera builds a skeleton of calcium carbonate (CaCO3), it incorporates O16 and O18 in a proportion that depends on the ratio in which they occur in the ambient water, and on the temperature of the water. The higher the temperature, the less O18 is put into the skeleton. If the ratio of the isotopes has remained constant in the oceans, then the ratios of such isotopes in a foraminiferal shell are a direct indication of temperature. The isotopic composition of the seas, however, has not remained constant, and the ratios in the shells can be disturbed by chemical changes after burial, but paleoecologists have demonstrated, for example, that the thermal structure of the oceans in Cretaceous times was much different from what it is today, with much warmer midwater masses.