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In 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 CH₄dynamics to primary productivity at the ecosystem scale or considered how the response may vary across lakes. Here, we investigate relationships between lake CH₄dynamics 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 CH₄storage rates for each lake using timeseries of hypolimnetic CH₄concentration through the summer season. Across all lakes and years, hypolimnetic CH₄storage ranged from <0.001 to 7.6 mmol CH₄ m⁻² d⁻¹and 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 CH₄storage 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 CH₄dynamics 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.