The Pantanal is one of the world’s largest freshwater wetlands. The spatial and temporal variability of flooded areas is a key factor for preserving and managing the flora and fauna of this biodiversity hotspot, and thus, its dynamic is crucial to maintain ecosystem services. However, existing inventories of flooded areas with high spatial resolution are scarce or do not represent a continuous time series considering the entire Pantanal wetland. In this study, flooded areas were derived from Landsat and Resourcesat satellite imagery time series for the years 2000 to 2020 through big data analytical tools. Our results show that permanently flooded areas accounted for 3.40% of the total Pantanal wetland and 8.85% of the study area was flooded during only one year, indicating a complex and dynamic fluvial system. In addition, approximately 39% of the basin was composed of non-flooded areas. During the analyzed period (2000–2020), the highest flood event occurred in 2011 covering an area of 57,969 km2, followed by 2014, with 52,500 km2 (respectively 38.55% and 34.91% of the total area of the Pantanal). The year with the smallest flooded area was 2020 (10,668 km2), 83% lower when compared to the period-based average. The Pantanal is a seasonal wetland, thus, rainfall plays a significant role in the flood pulse, accounting for approximately 60% of the total variability of the flooded areas. The flood dynamics is also affected by the morphology of the modern depositional system of the Pantanal, which is composed by large megafans created by several distributive rivers, and by neotectonics that generates differential movements of blocks creating lower areas that will determine how flood pulse moves spatially and temporally. Therefore, the understanding and analysis of this dynamism becomes an indispensable tool for the public government ordering defining policies for the occupation and the economic zoning of the Pantanal.