Knowledge of biodiversity in the past, and the timing, nature, and drivers of human-induced ecological change, is important for gaining deep time perspectives and for modern conservation efforts. The Marquesas Islands (Polynesia) are one of the world’s most remote archipelagos and illustrate the vulnerability of indigenous bioscapes to anthropogenic activities. Characterised by high levels of endemism across many biotic groups, the full spectrum of the group’s flora and fauna is nonetheless incompletely known. Several centuries of Polynesian settlement reshaped biotic communities in ways that are not yet fully understood, and historically-introduced mammalian herbivores have devastated the indigenous lowland flora. We report here on archaeological recovery of a diverse assemblage of plant and arthropod subfossils from a waterlogged deposit on the largest Marquesan island: Nuku Hiva. These materials offer new perspectives on the composition of lowland plant and arthropod communities pene-contemporaneous with human arrival. Bayesian analysis of multiple 14C results from short-lived materials date the assemblages to the mid-12th century AD (1129–1212 cal. AD, 95.4% HPD). Evidence for human activities in the catchment coincident with deposit formation includes Polynesian associated arthropods, microcharcoal, and an adzed timber. Plant macrofossils (seeds, fruits, vegetative structures) and microfossils (pollen, phytoliths) reveal coastal and lowland wet-moist forest communities unlike those observed today. Several apparently extinct taxa are identified, along with extant taxa currently constrained to high altitude and/or interior areas. A diverse inventory of subfossil arthropods—the first pre-18th century records for the islands—includes more than 100 distinct taxa, with several new archipelago records and one previously unreported for eastern Polynesia. The assemblages provide new insights into lowland Marquesan forest communities coincident with human arrival, and portend the considerable anthropogenic transformations that followed. These records also have implications for human colonisation of the Marquesas Islands and East Polynesia at large.