A field study was conducted in the Prairie Pothole Region of North Dakota to examine potential effects of localized subsurface drainage systems on wetland hydrology. As part of discrete studies utilizing the study sites (wetland catchments) from this study, samples of wetland surface water and subsurface drainage system effluent were collected from 2013–2016 and analyzed for standard water-quality variables (ions, elements, nutrients), agricultural chemicals (herbicides, pesticides), and metals. This data release presents water-quality data associated with these samples. Surface-water samples were collected from five wetlands and effluent was collected from the two drainage-system outlets from wetland Beck 6 and the lone outlet from wetland Beck 5. The number and frequency of samples were constrained by the lack of effluent from the subsurface drainage systems, as well as by the fact the wetlands only contained surface water during portions of the study. Formal analyses were not conducted on these data due to low sample replication and since the data were intended for inclusion in discrete studies. Qualitative examination of the standard water-quality data (e.g., ions, elements, nutrients) suggested that the ratio and concentrations of the dominant ions and elements varied temporally in conjunction with wetland water levels, as well as among wetlands and water sources (surface water, effluent). Similar variability was observed for nutrients (e.g., ammonia) and other water-quality variables such as total dissolved solids and pH. In addition to the standard water-quality variables, water samples were analyzed for 93 agricultural chemicals and metals, and concentrations of seven of these analytes were above the laboratory reporting limit for at least one sample; thus, a majority of the analytes were considered non-detects. The seven detected analytes represent common agricultural herbicides.