Lakes are known to be important to the global carbon balance as they are both CO₂ sources to the atmosphere and also accumulate large amounts of carbon in their sediment. CO₂ flux dynamics across the air–water interface in 11 lakes of varying trophic state in the Rotorua region, New Zealand, derived from measured alkalinity, pH and wind speed at given temperature, showed that lakes may shift from being atmospheric CO₂ sources to sinks due to seasonal changes in phytoplankton productivity and lake mixing dynamics. Decreases in trophic state (i.e. improved water quality) in some of the lakes over the eight-year monitoring period were associated with increased surface water CO₂ concentrations and, as a consequence, increased CO₂ flux to the atmosphere. Organic carbon content analysis of the bottom sediments revealed that lakes with high phytoplankton productivity, indicated by high chlorophyll a biomass, generally had high rates of carbon deposition to the sediments, but not all deposited carbon was permanently buried. Remineralization of the organic carbon accrued in productive lakes may potentially generate CO₂, as well as CH₄, which promotes these lakes to act as greenhouse gas emitters.