The spatial and temporal scales of marine biomonitoring are often constrained by the time and expense involved in carrying out ecological surveys. The lack of marine ecological data which spans across both temporal and spatial axes, limits the utility of marine biomonitoring for adaptive marine management. The Molecular Autonomous Planktonic Sampler (MAPS) is an autonomous eDNA sampler developed by the Ocean Technology and Engineering group at the National Oceanography Centre, designed to enable sampling at high resolution spatio-temporal scales. In this study we use qPCR and multi-marker metabarcoding, to compare the abundance of unicellular N2-fixing cyanobacteria group A (UCYN-A) and microbial and metazoan community composition, in samples collected simultaneously, using traditional ‘best practice’ methods for eDNA and autonomously using the MAPS device. The MAPS device successfully sampled across a range of biomass from oligotrophic open ocean to costal bloom conditions, with results comparable to those collected using traditional best practice methods. Easy to deploy autonomous eDNA samplers, such as the MAPS device can make it possible to collect high resolution time-series data at ocean observatories and deployment on ships of opportunity can vastly expand the spatial extent of eDNA biomonitoring.