Coastal ecosystems are some of the most biologically diverse and productive marine ecosystems on Earth. But direct human impacts at local scales combine with increasing climate-driven disturbances to fundamentally restructure these important ecosystems. As such, there is critical need to understand ecosystem complexity and establish holistic baselines to monitor species changes. Combining eDNA with traditional surveys allows the simultaneous assessment of occurrence and distribution of diverse organisms across trophic levels and domains of life at the ecosystem scale. Here we coupled six eDNA metabarcoding assays (MiFish, 16SFish, COI, 23S, 18S, ITS2) with diver-based fish surveys, Structure-from-Motion benthic surveys and airborne remote sensing on Hawai’i Island to quantify spatially-explicit and integrated metrics of coral reef ecosystem biodiversity. Coupled surveys detected >300 species of reef fishes and more than 1000 unique taxa of algae, zooplankton, and benthic invertebrates across 80 reefs spanning the west coast of Hawai’i Island. We leverage a unique dataset of human and environmental drivers to understand spatial patterns in diversity and abundance across biological levels from haplotypes to species to whole communities. We are developing a robust statistical framework for jointly modeling multi-marker eDNA and visual surveys to generate integrated metrics of fish and whole-reef biodiversity and upscale those products to the regional seascape. Coupling these approaches holds promise for enhancing biomonitoring across levels of biodiversity and informing ecosystem-based management of marine ecosystems.