Many organisms have free-running circadian clocks to anticipate the time of the day, including the Kai protein-based clock in the cyanobacterium Synechococcus elongatus. However, other species have an ‘hourglass’ timer, such as the cyanobacterium Prochlorococcus marinus. What conditions favor an hourglass timer or a free running clock over the other? We argue that this evolutionary choice is influenced by the noise levels in the external environment (e.g., light fluctuations due to weather) relative to noise levels in the internal environment of the cell (e.g., molecular fluctuations). Besides different clock dynamics in different species, we find that the clock of a single species, S. elongatus, exploits a clock-metabolic coupling to tune its clock dynamics towards an hourglass timer to deal with changing noise levels.