Trace fossils in estuarine deposits of different ages have been compared to evaluate colonization history of brackish-water ecosystems and to calibrate trace-fossil, brackish-water models with respect to geologic time. This comparative analysis reveals that, although the colonization of marginal-marine, brackish-water environments was a long-term process that spanned most of the Phanerozoic, this process of invasion of fully marine organisms into restricted, marginal-marine habitats did not occur at a constant rate.

Five major colonization phases can be distinguished. The first phase (Ediacaran–Ordovician) represents a prelude to the major invasion that occurred during the rest of the Paleozoic. While Ediacaran–Cambrian ichnofaunas seem to be restricted to the outermost zones of marginal-marine depositional systems, Ordovician assemblages show some degree of landward expansion within brackish-water ecosystems. Intensity of bioturbation and ichnodiversity levels were relatively low during this phase. The second phase (Silurian–Carboniferous) is marked by the appearance of more varied morphologic patterns and behavioral strategies, resulting in a slight increase in ichnodiversity. While previous assemblages were arthropod dominated, brackish-water Silurian–Carboniferous ichnofaunas include structures produced by bivalves, ophiuroids, and polychaetes. Ichnofaunas from the third phase (Permian–Triassic) seem to be characterized by the presence of crustacean burrows, reflecting the late Paleozoic crustacean radiation and adaptation of some groups to brackish-water conditions. The fourth phase (Jurassic–Paleogene) is typified by a remarkable increase in ichnodiversity and intensity of bioturbation of estuarine facies. Colonization occurred not only in softgrounds and firmgrounds, but also in hardgrounds and xylic substrates. The fifth phase (Neogene–Recent) records the onset of modern brackish-water benthos. Although still impoverished with respect to their fully marine counterparts, brackish-water ichnofaunas may reach moderately high diversities, particularly in middle- and outer-estuarine regions, and degree of bioturbation may be high in certain estuarine subenvironments. Comparative analysis of brackish-water ichnofaunas through geologic time provides valuable evidence to understand colonization of marginal-marine environments through the Phanerozoic, and allows for calibration of ichnologic models that may aid in the recognition of estuarine valley-fill deposits in the stratigraphic record.