Abstract Satellite altimetry is advantageous for measuring water surface elevations (WSE) globally. However, biases of time series can be caused by uneven water surfaces, as nadir pointing measurements are often collected at different locations across a lake. This study demonstrates how two‐dimensional WSE difference maps derived from the SWOT mission can enhance ICESat‐2 WSE time series. First, the SWOT‐derived WSE difference maps showed strong agreement with in situ data over Lake Erie (R2 = 0.79). For Lake Powell, this method improves the R2 of the ICESat‐2 time series from 0.62 to 0.89. Furthermore, spatial variability in water surface, as estimated using SWOT data, accounts for 44% and 16% of the uncertainty in median WSE fluctuations in global lakes and reservoirs, respectively. By analyzing 81,133 lakes worldwide, this study identifies hotspots of bias and offers an advantage for integrating multi‐satellite altimetry data, facilitating more accurate and long‐term hydrological monitoring across diverse global landscapes.