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There is growing interest in analyzing interdisciplinary datasets to better understand the evolution of ecosystems through deep time. One burgeoning area has been the integration of archaeological and fossil data to evaluate the long-term structure and function of habitats, floral and faunal communities, and ecosystems. Here, marine invertebrate data from Holocene archaeological sites and Pleistocene marine terrace deposits on California's Northern Channel Islands are combined to glean insights into the long-term structure of nearshore marine ecosystems, the composition of intertidal marine invertebrate communities, and the formation of archaeological shell middens. While a variety of methodological, analytical, and taphonomic challenges in comparing disparate datasets from fossil and archaeological contexts were identified, we offer perspectives for surmounting these challenges in future research. These findings indicate that the integration of fossil and archaeological data, spanning tens of thousands of years, offers important insights on the evolution of nearshore coastal ecosystems and marine climate change in California and around the world.