These data represent surface water and bed sediment samples analyzed for a variety of organic compounds. The samples were collected in streams and rivers in the Chesapeake Bay watershed from 2012-2018. Sites were located in Maryland, Pennsylvania, and West Virginia. Surface water samples were collected from 25 sites and analyzed for estrogenicity and an extensive suite of organic contaminants including hormones, pharmaceuticals, wastewater indicators, pesticides, phytoestrogens, and mycotoxins. Bed sediment samples were collected from 20 sites and analyzed for a suite of organic contaminants including hormones, wastewater indicators, pesticides, and organohalogens. Bed sediment was also analyzed for total organic carbon. Data also include replicate and blank quality assurance samples. This U.S. Geological Survey (USGS) data release contains daily-mean streamflow and water-quality data in the Chesapeake Bay watershed ranging from 2012 to 2018 (beginning and end dates may vary).