This dataset provides discrete nutrient, dissolved and greenhouse gas samples collected during ship-based cruises in the southern Great Barrier Reef lagoon, Australia. Here we sampled the greenhouse gases of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) with time matched (georeferenced samples) discrete nutrient measurements (dissolved organic carbon, ammonium, nitrate, dissolved inorganic nitrogen, total nitrogen and phosphate) collected from the lagoon. Nutrient concentrations remained low overall, while the lagoon was oversaturated in CO2 and CH4 despite highly oxygenated waters that are normally unconducive for CH4 production. N2O was also undersaturated in the oligotrophic conditions. Dissolved greenhouse gases were measured with a Picarro G2201-i Cavity Ring Down Spectrometer for CO2 (200 ppb ±0.05%) and CH4 (5 ppb ± 0.05%) and a Picarro G2308 Cavity Ring Down Spectrometer for N2O concentrations (<3.5 ppb ± 0.008%). Both Cavity Ring Down Spectrometer instruments were connected in a closed loop with twin showerhead exchangers and a gas drying agent (Drierite). The showerhead exchangers received seawater from the vessel cold water intake. Both instruments averaged 300 measurements over a five-minute cycle for each greenhouse gas sample. Salinity and temperature were recorded at the inlet of the seawater intake system with a Seabird SBE 21 (salinity ± 0.005 psu, temperature ± 0.002 °C). Dissolved oxygen was also recorded using a Hydrolab MS5 (dissolved oxygen 0.1 ± 0.02 mg L-1) fitted with an inline flow cell. Discrete nutrient and dissolved organic carbon (DOC) water samples were collected along survey transects using Niskin bottles from a depth of ⁓3 m. Dissolved nutrient samples were collected by filtering sample water through cellulose acetate syringe filters (0.45 µm) into sample rinsed 12 mL polypropylene vials before immediate freezing until laboratory analysis. Nutrient concentrations were determined using a Lachat QuickChem 8500 Flow Injection Analyser [Detection limits were 0.07 μmol ± 0.3% for nitrate (NOx-) and 0.35 μmol ± 5% for ammonium (NH4+)]. DOC samples were collected by filtering sample water through Whatman G/FF syringe filters (0.7 μm) into 40 ml pre-treated (100 μL mercuric chloride) VOC vials before immediate refrigeration until laboratory analysis. DOC concentrations were determined with OI Aurora 1030 W TOC Analyzer.