Two commercially available nanocalorimeters were assessed for direct measurement of respiration rates of micro-organisms in natural waters or liquid cultures as a function of temperature. Respiration heat rates were measured with isothermal and temperature-scanning nanocalorimeters in natural seawater and in cultures of microplankton and bacteria. The standard deviation of a measurement of metabolic heat rate by isothermal nanocalorimetry is ±25 nW/mL and by temperature-scanning nanocalorimetry, ±150 nW/mL as a continuous function of temperature. Although the absolute uncertainty of temperature scanning calorimetry is larger, the relative noise between data points is small and temperature scanning rapidly produces a curve of heat rate versus temperature that describes the metabolic response to temperature. Used together, the two methods are capable of generating a curve of metabolic heat rate versus temperature over the entire temperature range of respiratory activity in about 4 h.