Abstract  A method to estimate net community metabolism (NCM) in natural waters using vertical profiles of water temperature, salinity, dissolved O₂, gas tension, and calculated dissolved N₂ is presented. The method utilizes the disparate biological activity of dissolved O₂ and N₂ to estimate metabolism at different depths in the water column. For well-mixed surface waters, N₂ saturation levels are assumed to be the result of a quasi steady state balance of net warming or cooling and air–water gas exchange. Dissolved O₂ levels are assumed to maintain a similar balance, subject to net biological activity, and NCM is then calculated based on the difference between N₂ and O₂ saturation levels and the estimated timescale required to equilibrate the layer with the atmosphere. For deeper stratified layers of water that warmed after layer formation in isolation from the atmosphere, the temperature at formation is calculated using the measured N₂ concentration and an assumed N₂ saturation level of 100% at formation. By assuming that initial N₂ and O₂ saturation levels were equal, the initial O₂ concentration is calculated based on solubility relationships. NCM of the deeper waters is then estimated based on this information and knowledge of the general seasonal heating cycle of the waters. Daily mean water temperature and dissolved gas levels are used in the calculations. The method was assessed using profile measurements collected at Long Pond, Plymouth, Massachusetts, USA, on 23 August 2002. Oxygen was supersaturated relative to N₂ by approximately 4% in the 0–6 m deep epilimnion, and undersaturated relative to N₂ by approximately 7% in the stratified water at 9 m depth. The estimated 4-day average NCM for the epilimnion was 140 ± 70 mgC m⁻²day⁻¹. For waters at 9 m depth, the temperature at formation was calculated to be 6.58 °C, and the estimated 100-day average NCM was −2.5 ± 0.6 mgC m⁻³ day⁻¹. An independent estimate of −4.6 ± 0.9 mgC m⁻³ day⁻¹ was derived from the measured O₂ decline at 9 m depth over the same period of 2003.