There is growing awareness of the need to better constrain the contribution of atmospheric methane (CH4) fluxes from urbanized estuaries due to the high global warming potential of CH4 and the accelerating growth of urban expansion. This study undertook seasonal sampling campaigns to understand the impact of urbanization on atmospheric CH4 fluxes and their drivers in a large, tropical estuary in India. Overall, the study found that the Cochin estuary emitted large amounts of CH4 (398.8 ± 141.6 μmolm−2d−1) to the atmosphere with CH4 hotspots reaching up to 939.7 μmolm−2d−1 were identified. The strongest drivers of CH4 dynamics in different anthropogenically impacted zones were traced. The source of organic matter for CH4 production was revealed to be terrestrial C3 plants, autochthonous production, marine phytoplankton, and sewage inputs. The study suggests that monsoonal urbanized tropical estuaries may be an important but under-recognized element of the global CH4 budget. Display omitted •CH4 fluxes increased thirty-two fold and were higher than in many European estuaries.•CH4 hotspots correspond to regions highly affected by anthropogenic interventions.•Urbanized tropical estuaries are an under-recognized element of the global CH4 budget.