Measurement of diel changes in dissolved gases within the lake, also known as the "free-water" method, has quickly become the most common method of estimating lake metabolism since the wide adoption of autonomous sensors used to measure dissolved oxygen and carbon dioxide in water. The free-water method is particularly popular since many daily estimates of lake metabolism can be collected relatively cheaply and can give insights into metabolic regimes during difficult-to-observe time periods, such as during storm events. Measured changes in dissolved oxygen and carbon dioxide within a lake represents the sum of all organismal metabolism from bacteria to fishes, after accounting for abiotic changes in dissolved gases. Abiotic changes in dissolved gases include exchanges of dissolved gases between the atmosphere and lake surface, vertical or horizontal entrainment of water with differing concentrations (e.g. low-oxygen water below a lake's thermocline), or import and export of dissolved gases from inflowing streams or a lake outlet. Abiotic changes in dissolved gases can dominate changes of dissolved gases if the lake has a low metabolic rate (e.g. oligotrophic lake, cloudy day), or if there is a large event that causes abiotic factors to exceed biotic (e.g. wind event causing mixing and entrainment of low-oxygenated water). Biotic signals in dissolved gases are most evident when the sun is shining and photosynthesis is occurring, resulting in the production of dissolved oxygen and consumption of carbon dioxide. The conversion of solar energy to chemical energy is termed gross primary production (GPP) and the dissipation of this energy through biological carbon oxidation is termed ecosystem respiration (ER). High-frequency (e.g. 10 minute interval) measurements of dissolved oxygen or carbon dioxide can be translated into estimates of GPP, ER, and the difference between the two termed Net Ecosystem Production (NEP), by fitting the high-frequency data to models of lake metabolism. The governing equation for estimating lake metabolism from a single sensor located in the upper mixed layer  measuring dissolved oxygen is:
DO/t = GPP-ER+F
Where F is the flux of gases between the lake and the atmosphere. Additional terms of abiotic gas flux can be added if those abiotic fluxes are deemed significant for a lake (e.g. mixing events, inflowing stream gases). Atmospheric gas exchange (F) is rarely directly measured and typically modeled by estimating lake surface turbulence from wind-driven and convective mixing. Most often, F is estimated from measurements of wind speed and atmospheric pressure, and different models for estimating F can result in significantly different estimates of lake metabolic rates depending on the study lake. Gross primary production is assumed to be zero during the night due to low or no light, and thus ER can be estimated from nighttime changes in dissolved oxygen (or carbon dioxide) after accounting for abiotic changes in dissolved oxygen. Gross primary production can be estimated assuming that ER is equal during the day and night and accounting for dissolved oxygen changes during the day, however, this assumption may not be valid in every lake.
Extracting a high signal-to-noise ratio is key to obtaining good estimates of lake metabolism from the free-water technique, and there are choices that a researcher needs to make prior to collection data and during data analyses to ensure accurate estimates. Location of dissolved gas collection (typically in the surface mixed layer), number of sensors vertically and horizontally, frequency and duration of data collection, and modeling methods need to be considered.