<p>Anthropogenic activities have led to increased methane production in lakes and inland water bodies, contributing to atmospheric methane levels. While there is considerable research on methane emissions, their ecological impact, particularly on species interactions, remains underexplored. Unlike organic contaminants, methane does not bioaccumulate in the food web, which makes its effects on species harder to elucidate. Though it serves as an alternative carbon source for plankton, at higher concentrations, it depletes dissolved oxygen levels. Here we develop a methane–plankton–detritus model to investigate the ecological effects of methane in aquatic ecosystems. We perform bifurcation analysis to estimate the thresholds under which methane acts as a food resource or a stressor. Our results show increased abundance of plankton at low to moderate methane concentrations. At elevated methane levels, however, methane acts as a stressor to zooplankton that reduces their abundance, while phytoplankton growth remains unaffected. Prolonged exposure to methane modulates the thermal tolerance of phyto- and zooplankton. To investigate the population dynamics in methane-enriched lakes, we perform multiscale analysis. We show rapid release of methane slows zooplankton growth, leading to long transient characterized by crawl-by regime. It leads to prolonged suppression of zooplankton populations even when methane concentration stabilizes, emphasizing on a long-lasting trophic imbalance. Our bottom-up modelling yields novel insight into how methane release will shape aquatic ecological outcomes and provides a framework for understanding the role of methane in ecosystems under changing environmental conditions.</p>