Freshwater environments contribute 75% of the natural global methane (CH4) emissions. While there are indications that tropical lakes and reservoirs emit 58?400% more CH4 per unit area than similar environments in boreal and temperate biomes, direct measurements of tropical lake emissions are scarce. We measured CH4 emissions from 16 natural shallow lakes in the Pantanal region of South America, one of the world?s largest tropical wetland areas, during the low water period using floating flux chambers. Measured fluxes ranged from 3.9 to 74.2 mmol m?2 d?1 with the average from all studied lakes being 8.8 mmol m?2 d?1 (131.8 mg CH4 m?2 d?1), of which ebullition accounted for 91% of the flux (28?98% on individual lakes). Diel cycling of emission rates was observed and therefore 24-h long measurements are recommended rather than short-term measurements not accounting for the full diel cycle. Methane emission variability within a lake may be equal to or more important than between lake variability in floodplain areas as this study identified diverse habitats within lakes having widely different flux rates. Future measurements with static floating chambers should be based on many individual chambers distributed in the various subenvironments of a lake that may differ in emissions in order to account for the within lake variability.2010