The accuracy of sea surface heights (SSHs) estimation from satellite altimeters is strongly influenced by the microwave reflected signals (or waveforms). Waveforms in open oceans generally have ideal shapes following the Brown (1977) model. However, in coastal and shallow waters, the signals are disturbed by lands, thus resulting in complicated waveforms (non-Brown). Non-Brown waveforms produce inaccurate SSH estimations; therefore, specialized protocols such as waveform classification and retracking are crucial when attempting to produce accurate estimations. In this study, waveforms of Jason-2 and Jason-3 satellite altimeters in the Halmahera were classified and retracked using several algorithms, such as Offset Centre of Gravity (OCOG), Ice, Threshold, and Improved Threshold. The results showed that waveforms in the Halmahera Sea had ten generic classes with dominant class of the Browns. The validation results showed that all retrackers (except OCOG) had the value of correlations exceeding 0.75, and Root Mean Square Error (RMSE) smaller than 25 cm at a distance of 5-20 km from the land. The Threshold 10% was the most common retracker that appeared with the highest improvement percentage (IMP), meanwhile the Ice retracker consistently produced the best correlation (0.86) and the lowest RMSE (16cm). The retracking results showed that waveform retracking generally can improve SSH estimation accuracy from ocean (standard) retracker.