A new method to autonomously collect larvae and environmental variables such as temperature, salinity, and circulation is described. A large volume in situ pumping system, recently developed for discrete biogeochemical sample collection in deep-sea environments, was adapted and mounted to the autonomous underwater vehicle (AUV) REMUS 600 for autonomous larval and environmental sampling in coastal waters. To assess the performance of this system, the distribution of barnacle larvae was assessed in March 2014 with two transects perpendicular to the coastline (~ 9.9 and 11.2 km) in Buzzards Bay, Massachusetts, USA. The second transect included a complex sampling mission through a relatively deeper channel, and sampling at discrete depth intervals. In this deployment, nearshore and surface waters were fresher, with distinct vertical stratification due to salinity. Barnacle larvae were classified into early nauplii, late nauplii, and cyprid stages, and the mitochondrial COI barcode marker was sequenced to identify individual larvae of different stages. In an analysis of 164 barcode sequences, larvae belonging to Amphibalanus sp., Semibalanus balanoides, and Chthamalus fragilis were found, with Amphibalanus sp. the most abundant larval taxon overall. In the second deployment, early and late nauplii were relatively more abundant near the bottom. However, there was no obvious pattern relative to depth with cyprids, and there were no clear cross-shore distributional patterns for nauplii and cyprids. While additional deployments are necessary to corroborate these observations, the results demonstrate the feasibility of this approach. Autonomous vehicle based sampling has the potential to collect larvae of other invertebrates as well as zooplankton, and together with genetic identifications, overcomes many existing limitations and will provide valuable new insight in understanding larval distributions and transport dynamics.