Wetlands in drylands are vulnerable to degradation and disappearance due to the combined effects of increasing anthropogenic disturbances and climatic extremes. Such influences may drive non-linear shifts in surface responses that require long-term monitoring approaches for their study. Here, we used a piece-wise regression model to characterize long-term Ecosystem Change Types (ECT) in the surface water and vegetation dynamics of the Inner Niger Delta wetlands in Mali between 2000 and 2019. We also examined the added benefits of using a dense Landsat time series for such segmented trend analysis in comparison with MODIS products that are regularly used for ecosystem trends assessment. Our approach has found statistically significant (p < 0.05) long-term changes in wetland ecosystems, as calculated from Modified Normalized Difference Water Index (MNDWI) and Normalized Difference Vegetation Index (NDVI) image series on both the MODIS and the Landsat scales. The class-specific accuracies of the detected ECTs were evaluated through the validation of temporal trajectories based on the TimeSync logic at selected probability sample locations. Results showed higher user's, producer's, and overall accuracies (OA) when using a dense Landsat time series (OA = 0.89 ± 0.01), outperforming the MOD09A1 time series (OA = 0.37 ± 0.03). Our study provides a robust framework for long-term wetland monitoring that demonstrates the benefits of applying dense Landsat time-series imagery for accurate quantifications of linear and non-linear ecosystem responses in vast highly dynamic floodplain systems. Delivering such an improved assessment, in a spatial resolution that better resolves the characteristics of wetlands ecosystems, has the potential to support the information needs of global conservation and restoration efforts.