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Dissolved oxygen controls important processes in lakes, from chemical reactions to organism community structure and metabolism. In shallow lakes, small volumes allow for large fluctuations in dissolved oxygen concentrations, and the oxygen regime can greatly affect ecosystem‐scale processes. We used high frequency dissolved oxygen measurements to examine differences in oxygen regimes between two alternative stable states that occur in shallow lakes. We compared annual oxygen regimes in four macrophyte‐dominated, clear state lakes to four phytoplankton‐dominated, turbid state lakes by quantifying oxygen concentrations, anoxia frequency, and measures of whole‐lake metabolism. Oxygen regimes were not significantly different between lake states throughout the year except for during the winter under‐ice period. During winter, clear lakes had less oxygen, higher frequency of anoxic periods, and higher oxygen depletion rates. Winter oxygen depletion rates correlated positively with peak summer macrophyte biomass. Due to lower levels of oxygen, clear shallow lakes may experience anoxia more often and for longer duration during the winter, increasing the likelihood of fish winterkills. These observations have important implications for shallow lake management, which typically focuses efforts on maintaining the clearwater state.