Accurately monitoring and predicting the large-scale dynamic changes of water levels in coastal zones is essential for its protection, restoration and sustainable development. However, there has been a challenge for achieving this goal using a single radar altimeter and retracking technique due to the diversity and complexity of coastal waveforms. To solve this issue, we proposed an approach of estimating water level of the coastal zone in Beibu Gulf, China, by combination of waveform classifications and multiple sub-waveform retrackers. This paper stacked Random Forest (RF), XGBoost and CatBoost algorithms for building an ensemble learning (SEL) model to classify coastal waveforms, and further evaluated the performance of three retracking strategies in refining waveforms using Cryosat-2, SARAL, Sentinel-3 altimeters. We compared the estimation accuracy of the coastal water levels between the single altimeter and synergistic multi-altimeter, and combined Breaks for Additive Season and Trend (BFAST), Mann-Kendall mutation test (MK) with Long Short-Term Memory (LSTM) algorithms to track the historical change process of coastal water levels, and predict its future development trend. This paper found that: (1) The SEL algorithm achieved high-precision classification of different coastal waveforms with an average accuracy of 0.959, which outperformed three single machine learning algorithms. (2) Combination of Threshold Retracker and ALES+ Retracker (TR_ALES+) achieved the better retracking quality with an improvement of correlation coefficient (R, 0.089~0.475) and root mean square error (RMSE, 0.008∼ 0.029 m) when comparing to the Threshold Retracker & Primary Peak COG Retracker and Threshold Retracker & Primary Peak Threshold Retracker. (3) The coastal water levels of Cryosat-2, SARAL, Sentinel-3 and multi-altimeter were in good agreement (R>0.66, RMSE<0.135m) with Copernicus Climate Change Service (C3S) water level. (4) The coastal water levels of the Beibu Gulf displayed a slowly rising trend from 2011 to 2021 with an average annual growth rate of 8mm/a, its lowest water level focused on May-August, the peak of water level was in October-November, and the average annual growth rate of water level from 2022-2031 was about 0.6mm/a. These results can provide guidance for scientific monitoring and sustainable management of coastal zones.