This dataset includes physical, chemical, and biological water sampling data collected in Saginaw Bay, Lake Huron from 2008 to 2010. These data were collected to aid in the understanding of nutrient loading, harmful algal blooms (HABs), and beach health of the Saginaw Bay ecosystem. Water samples were collected 0.5 m below the surface in 500 mL acid-washed bottles pre-rinsed with sample water, stored at 4 °C in the dark, and processed within 24 hours. Water parameters analyzed include Secchi depth, temperature, particulate Microcystin, extracted Chlorophyll-a, total phosphorus, total dissolved phosphorus, soluble reactive phosphorus, ammonia, nitrate + nitrite, dissolved silica, chloride, particulate organic carbon, particulate organic nitrogen, dissolved organic carbon, total suspended solids, and volatile suspended solids. Conductivity, temperature, and depth (CTD) casts were collected during each field sampling. Some of the casts included sensors to collect chlorophyll fluorescence, dissolved oxygen, photosynthetically active radiation (PAR), and phycocyanin fluorescence.