This data set contains water quality data collected in an area important to shellfish aquaculture. The data collected are parameters such as fecal coliforms (fc), nutrients, and stable isotope ratios, salinity, dissolved oxygen, and others collected in West Fowl River and Portersville Bay, Alabama. These data contribute to identification and understanding of potential sources of water quality variation, which can inform modeling, further sampling, and enforcement efforts to improve the local water quality for recreation and aquaculture.