Concentrated (or confined) animal feed operations (CAFOs) are the principal means of livestock production in the United States, and such facilities pollute nearby waterways because of their waste management practices; CAFO waste is pumped from the confinement structure into a cesspit and sprayed on a field. Stocking Head Creek is located in eastern North Carolina, a state with >9,000,000 head of swine confined in CAFOs. This watershed contains 40 swine CAFOs; stream water quality was investigated at seven sites during 2016, with five sampling dates in early spring and five in summer. Geometric mean fecal coliform counts were in the thousands/100 mL at five sites in spring and all seven sites in summer. Excessive nitrate pollution was widespread with concentrations up to >11.0 mg N/L. Seasonality played an important role in pollutant concentrations. In North Carolina, spraying animal waste on adjoining fields is permissible from March 1 through September 30. Seasonal data showed significantly higher (p < 0.01) concentrations of conductivity, nitrate, total nitrogen, total organic carbon, and fecal bacteria in summer as opposed to early spring. Thus, sampling performed only in winter-early spring would significantly underestimate impacts from swine CAFO spray fields on nearby waterways.