AbstractIn lakes, the production and emission of methane (CH4) have been linked to lake trophic status. However, few studies have quantified the temporal response of lake CH4 dynamics to primary productivity at the ecosystem scale or considered how the response may vary across lakes. Here, we investigate relationships between lake CH4 dynamics and ecosystem primary productivity across both space and time using data from five lakes in northern Wisconsin, USA. From 2014 to 2019, we estimated hypolimnetic CH4 storage rates for each lake using timeseries of hypolimnetic CH4 concentration through the summer season. Across all lakes and years, hypolimnetic CH4 storage ranged from <0.001 to 7.6 mmol CH4 m−2 d−1 and was positively related to the mean summer rate of gross primary productivity (GPP). However, within‐lake temporal responses to GPP diverged from the spatial relationship, and GPP was not a significant predictor of interannual variability in CH4 storage at the lake scale. Using these data, we consider how and why temporal responses may differ from spatial patterns and demonstrate how extrapolating cross‐lake relationships for prediction at the lake scale may substantially overestimate the rate of change of CH4 dynamics in response to lake primary productivity. We conclude that future predictions of lake‐mediated climate feedbacks in response to a shifting distribution of trophic status should incorporate both varying lake responses and the temporal scale of change.