Water availability is vital for the sustenance of livelihoods in the Lake Chad Basin. However, the daily and seasonal dynamics of open water bodies are not well understood. This study aims to (1) analyze the daily and seasonal dynamics of water bodies, (2) estimate changes in surface water area extent including trends and change points, and (3) assess the connection between surface water extent and seasonal rainfall variation. To achieve this, we used the Global WaterPack and ERA5-Land daily aggregated datasets. We employed time series decomposition, trends analysis, and temporal lag correlation in our analysis. The results showed strong seasonal patterns of natural lakes compared to reservoirs/dams. Between 2003 and 2022, Lake Chad averaged 2,475.64 km−2. The Northern pool of Lake Chad exhibited significant fluctuations, remaining below 600 km² between 2005 and 2012, from 2016 to 2019), with less than 350 km2 lasting only for a few days annually. The Southern pool averaged between 2,200 and 2,400 km−2, except during drought years (2006–2007), specifically between the days of the year to approximately 66, and days 301–365/6. In Lake Fitri, the yearly maximum and minimum water extents were observed between days 1–59 and 305–365/6, and between days 60 and 304, respectively.