We reconstructed water quality changes for 1800 to 2000 in Charlotte Harbor (Florida), a shallow subtropical estuary, by using a suite of biological and geochemical proxies in dated sediments collected in the region of a present day, midsummer hypoxic zone. The declining freshwater loading into the estuary from 1931 to the 1980s is not the probable causal agent encouraging the appearance or expansion of a hypoxia zone (measuring up to 90 km2 in summer). Rather, the reconstructed trends in nitrogen loading indicate increased phytoplankton production has likely caused a decline in bottom water oxygen concentrations. Sedimentary biogenic silica (BSi), carbon, nitrogen, and phosphorus concentrations increased concurrently with known or inferred changes in nutrient loadings. There were direct relationships between phytoplankton pigments and BSi, heavier 34S with increased carbon loading, and sequestration of P, Al, and Fe as carbon loading increased. The results from the sediment analyses and the results from mixing models using C:N ratios and 13C suggest an estuarine system that is responsive to increased carbon loading from the nitrogen-limited phytoplankton community and whose sediments are becoming increasingly anoxic as a result. The present nitrogen loading is about three times above that prior to the 1800s, suggesting that without management intervention the anticipated doubling of the watershed's population from 1990 to 2020 will greatly increase the nitrogen loading to this estuary and will lead to much higher amounts of phytoplankton biomass and accumulation and exacerbate hypoxic conditions.