Restoration of the Chesapeake Bay, the largest estuary in the United States, is a national priority. Documentation of progress of this restoration effort is needed. A study was conducted to examine water quality in the Choptank River estuary, a tributary of the Chesapeake Bay that since 1998 has been classified as impaired waters under the Federal Clean Water Act. Multiple water quality parameters (salinity, temperature, dissolved oxygen, chlorophyll a) and analyte concentrations (nutrients, herbicide and herbicide degradation products, arsenic, and copper) were measured at seven sampling stations in the Choptank River estuary. Samples were collected under base flow conditions in the basin on thirteen dates between March 2005 and April 2008. As commonly observed, results indicate that agriculture is a primary source of nitrate in the estuary and that both agriculture and wastewater treatment plants are important sources of phosphorus. Concentrations of copper in the lower estuary consistently exceeded both chronic and acute water quality criteria, possibly due to use of copper in antifouling boat paint. Concentrations of copper in the upstream watersheds were low, indicating that agriculture is not a significant source of copper loading to the estuary. Concentrations of herbicides (atrazine, simazine, and metolachlor) peaked during early-summer, indicating a rapid surface-transport delivery pathway from agricultural areas, while their degradation products (CIAT, CEAT, MESA, and MOA) appeared to be delivered via groundwater transport. Some in-river processing of CEAT occurred, whereas MESA was conservative. Observed concentrations of herbicide residues did not approach established levels of concern for aquatic organisms. Results of this study highlight the importance of continued implementation of best management practices to improve water quality in the estuary. This work provides a baseline against which to compare future changes in water quality and may be used to design future monitoring programs needed to assess restoration strategy efficacy.