The dataset is from the South Florida Ecosystem Restoration Cruises on R/V Walton Smith and R/V Hogarth. Data has been collected bimonthly since 1998 at fixed stations along the Florida Reef Tract, Florida Bay and Southwest Florida. A CTD is deployed to collect in-situ water quality measurements and water samples at the sea surface. Water samples for nutrient analysis are filtered after collection using a 0.45 micromolar filter and frozen for the duration of the cruise. Water samples collected for chlorophyll-a analysis are filtered onto glass microfiber filters, with each filter stored in individual sample tubes and placed in liquid nitrogen for the duration of the cruise. All samples are brought back to the laboratory for analysis. Nutrient samples are analyzed for ammonium, phosphate, nitrate+nitrite, nitrite, and silicate on a SEAL AA3 Autoanalyzer following EPA methods and NELAC standards. Chlorophyll-a is analyzed on a fluorometer following EPA methods and NELAC standards. Temperature and salinity are measured in-situ using sensors attached to the CTD. Field duplicates are also collected and analyzed at a subset of stations to ensure quality control.