We evaluated three autonomous environmental DNA sequencers produced by Dartmouth Ocean Technologies Inc (Dartmouth, Canada) compared to time-at-sample Smith Root filters to determine each technology's performance for monitoring in the marine world. We deployed three autonomous samplers from DOT in the Bedford Basin (Canada) over a nine-week period in summer/fall 2023. The samplers sampled at programmed interviews over this time period, and we collected contemporaneous samples with a Smith-Root eDNA sampler by boat during each sampling period. Both eDNA sample types captured similar fish diversity, including typical diversity for the Northwest Atlantic. The invertebrate community detected using the COI marker was different between each sample type, likely due to differences in filter pore size. We found biofouling was minimal over the study period, even in a high-traffic area such as the Bedford Basin, likely due to the relatively short experimental period, and copper screening covering in the inlet and outlet valves of the instruments. Overall, our results show promise to deploy autonomous eDNA samplers in marine conservation areas to contribute to monitoring in the temperate ocean, but further testing over longer periods of time is needed to determine if DNA remains well-preserved in the autonomous samplers at ambient ocean temperatures. This work is published as part of the Oceans 2024 Halifax conference publication series.