This data release includes hydroacoustic data for the 2021 to 2022 water years at four stations. These stations are part of a discrete and continuous monitoring project in embayments on Long Island Sound to support nutrient management activities in Connecticut. The data were collected by the U.S Geological Survey (USGS) in cooperation with the Connecticut Department of Energy and Environmental Protection. The data were collected using acoustic doppler current profilers (ADCPs) sampling 134 parameters every six minutes. Recorded values above the water surface were removed from files using an R script. The ADCPs were deployed at upstream and downstream locations in the Mystic and Norwalk embayments. For the Mystic River embayment, the upstream station is the Mystic River at Mystic Seaport near Mystic, CT (412141071580200), USGS streamgage and the downstream station is the Mystic River at Ram Island Yacht Club at Noank, CT (411940071590300), USGS streamgage. For the Norwalk embayment, the upstream station is the Norwalk River at Norwalk Aquarium near South Norwalk, CT (410606073245700), USGS streamgage and the downstream station is the Norwalk Harbor at the Cove Marina near East Norwalk, CT (410502073236000), USGS streamgage. Data are provided for each station in a ‘zip’ file and each zip file includes a description for the station’s ADCP setup.