The methane (CH4) content of gas bubbles in sediments and CH4 emission from plants in the Pantanal wetland of Brazil was examined across a depth gradient to ascertain the relative importance of plant-mediated CH4 emission versus ebullition. Sediment bubbles contained >50% CH4 at sites with water depths >1 m but often contained <50% CH4 in shallower waters. Previous work has shown that bubble % CH4 is related to ebullition rates, and therefore these patterns are suggestive of greater CH4 emission by ebullition from deeper waters compared to waters <1 m in depth. Stable isotope ratios of carbon and hydrogen in the CH4 showed evidence for significant CH4 oxidation but no apparent relation with water depth. Shallower waters typically contain rooted emergent plants with erect, vertical stems or petioles, whereas in waters deeper than ~1 m, emergent aquatic plants are limited to rooted forms with long stems that float at the water surface. Rooted emergent plants typical of deeper waters had low rates of CH4 emission (0.0–0.2 mg d−1 CH4 for individual plants) compared to species typical of inundation depths <1 m (1.6–7.5 mg d−1 CH4). These observations suggest that tropical savanna floodplains like the Pantanal with inundation depths >1 m have low rates of CH4 emission via rooted emergent and floating-leaf plants, in contrast to results from shallower rice fields and temperate wetlands in which plant-mediated transport dominates CH4 emission from vegetated waters.