We extend the Dynamic Global Vegetation Model LPJmL to version 6.0 by explicitly representing methane (CH₄) dynamics within the coupled carbon–nitrogen–water system. The implementation (i) prognoses water-table depth and wetland extent using a CTI–TOPMODEL framework, (ii) solves sub-daily, vertically explicit mass balances for CH₄ and O₂ including diffusion, ebullition, and plant-mediated transport, (iii) represents methanogenesis and methanotrophy with temperature- and moisture-dependent kinetics, and (iv) integrates land-use and rice management effects alongside inundation-tolerant plant functional types. This architecture enables consistent simulation of CH₄, carbon dioxide (CO₂) and nitrous oxide (N₂) emissions from natural wetlands and managed systems together with the soil CH₄ sink. Extensive benchmarking against global datasets shows that LPJmL6 reproduces the magnitude and regional–temporal variability of CH₄ flux pathways while maintaining strong skill in the simulated terrestrial carbon, nitrogen, and water budgets. The model thus provides a coherent, process-based framework to quantify CH₄ within the coupled carbon–nitrogen–water system, elucidate interactions with vegetation and soils, and assess how land-use, wetland conservation and restoration, and rice management options affect methane and overall greenhouse–gas budgets in support of climate-mitigation strategies.