Water monitoring at four locations on the Choptank River and four locations on the Pocomoke River in Maryland, U.S.A., was conducted from 2021 through 2023. Funding and scientific rationale were provided by the National Science Foundation grant 2049073 (“Resolving Sediment Connectivity between Rivers and Estuaries by Tracking Particles with their Microbial Genetic Signature”). The monitoring locations were chosen to measure estuary dynamics from the tidal freshwater zone through the mesohaline estuary. Parameters measured included water temperature, water level, water conductivity (reported as specific conductivity), water turbidity, and water velocity.