<p>Biogenic methane, the largest contributor to atmospheric methane, is produced via different microbial methanogenic pathways, depending on the substrates and type of methanogens. Stable carbon and hydrogen isotope measurements (δ¹³C and δD) and the clumped isotopologues (Δ¹³CH₃D and Δ¹²CH₂D₂) of methane have emerged as important diagnostic tools, providing insights into methane sources and reaction pathways. Here, we investigate the pathway-specific bulk and clumped isotopic signatures of methane produced by microbial communities in sediments from a marine coastal system (lake Grevelingen, the Netherlands). Sediment batches were incubated with different substrates (acetate, carbon dioxide + hydrogen, methanol, and methanol + hydrogen) to promote the different methanogenic pathways. Our results show that the methanogenic pathways studied produce isotopically distinct methane. Analysis of the 16S rRNA gene from the sediment reveals a metabolically diverse methanogenic community capable of sustaining hydrogenotrophic, acetoclastic, and methylotrophic pathways, consistent with the isotopic variability observed in methane produced during incubations. The methylotrophic and acetoclastic pathways yield methane with significantly lower Δ¹²CH₂D₂ than the hydrogenotrophic pathway due to the combinatorial anti-clumping effect. The methane produced in situ in the sediments predominantly originates from the hydrogenotrophic pathway, with Δ¹³CH₃D and Δ¹²CH₂D₂ values closely matching incubations with carbon dioxide and hydrogen. Overall, the incubation results using lake sediments align well with previous pure culture studies, highlighting the potential of clumped isotope analysis to differentiate methane production pathways in natural environments.</p>