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Nhecolândia is a vast sub-region of the Pantanal wetland in Brazil with great diversity in surface water chemistry evolving in a sodic alkaline pathway under the influence of evaporation. In this region, more than 15,000 shallow lakes are likely to contribute an enormous quantity of greenhouse gas to the atmosphere, but the diversity of the biogeochemical scenarios and their variability in time and space is a major challenge to estimate the regional contribution. In this study, we compiled measurements of the physico-chemical characteristics of water and sediments, gas fluxes in floating chambers, and sedimentation rates to illustrate this diversity. Although these lakes have a similar chemical composition, the results confirm an opposition between the black-water and green-water alkaline lakes, corresponding to distinct biogeochemical functioning. Black-water lakes are CO2 and CH4 sources, with fairly constant emissions throughout the seasons. Annual carbon dioxide and methane emissions approach 790 mmol m-2 y-1 and 73 mmol m-2 y-1, respectively. By contrast, green-water lakes are CO2 sinks but significant CH4 sources with fluxes varying significantly throughout the seasons, depending on the development of the cyanobacterial bloom. The results highlight two hot moments for methane emissions. The first one is suspected after the disappearance of the cyanobacterial bloom, which is accompanied by a drop in pH of the upper part of the sediments. The second one is identified when the O2-supersaturation is reached under extreme bloom and sunny weather conditions, which provoke an abrupt O2 purging of the lakes. Taking into account the seasonal variability, annual methane emissions are around 8,850 mmol m-2 y-1, i.e., much higher than reported in previous studies for alkaline lakes in Nhecolândia. Carbon dioxide consumption is estimated about 1,140 mmol m-2 y-1. However, these balances must be better constrained with systematic and targeted measurements around these hot moments. [ABSTRACT FROM AUTHOR]