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The importance of monitoring sea level in coastal zones becomes more and more obvious in the era of global climate change, because, in coastal zones, although satellite altimetry is an ideal tool in measuring sea level over open ocean, but its accuracy often decreases significantly at coast due to land contamination. Although the accuracy of waveform processing algorithms for synthetic aperture altimeters has been improved in the last decade, the computational speed is still not fast enough to meet the requirements of real-time processing, and the accuracy cannot meet the needs of nearshore areas within 1 km from the coast. To improve the efficiency and accuracy in the coastal zone, this study proposed an innovative waveform retracking scheme for the coastal zone based on a multiple optimization parabolic cylinder algorithm (MOPCA) integrated with machine learning algorithms such as recurrent neural network and Bayesian estimation. The algorithm was validated using 153-pass repeat cycle data from Sentinel-6 over Qianliyan Island and Hong Kong–Wanshan Archipelago. The computational speed of the proposed algorithm was four to five times faster than the current operational synthetic aperture radar (SAR) retracking algorithm, and its accuracy within 0–20 km from the island was comparable to the most popular SAMOSA+ algorithm, better than the official data product provided by Sentinel-6. Especially, the proposed algorithm demonstrates remarkable stability in the sense of proceeding speed. It maintains consistent performance, even when dealing with intricate wave patterns within a proximity of 1 km from the coast. The results showed that the proposed scheme greatly improved the quality of coastal altimetry waveform retracking. [ABSTRACT FROM AUTHOR]