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Airborne or space-borne photon-counting lidar can provide successive photon clouds of the Earth's surface. The distribution and density of signal photons are very different because different land cover types have different surface profiles and reflectance, especially in coastal areas where the land cover types are various and complex. A new adaptive signal photon detection method is proposed to extract the signal photons for different land cover types from the raw photons captured by the MABEL (Multiple Altimeter Beam Experimental Lidar) photon-counting lidar in coastal areas. First, the surface types with 30 m resolution are obtained via matching the geographic coordinates of the MABEL trajectory with the NLCD (National Land Cover Database) datasets. Second, in each along-track segment with a specific land cover type, an improved DBSCAN (Density-Based Spatial Clustering of Applications with Noise) algorithm with adaptive thresholds and a JONSWAP (Joint North Sea Wave Project) wave algorithm is proposed and integrated to detect signal photons on different surface types. The result in Pamlico Sound indicates that this new method can effectively detect signal photons and successfully eliminate noise photons below the water level, whereas the MABEL result failed to extract the signal photons in vegetation segments and failed to discard the after-pulsing noise photons. In the Atlantic Ocean and Pamlico Sound, the errors of the RMS (Root Mean Square) wave height between our result and in-situ result are −0.06 m and 0.00 m, respectively. However, between the MABEL and in-situ result, the errors are −0.44 m and −0.37 m, respectively. The mean vegetation height between the East Lake and Pamlico Sound was also calculated as 15.17 m using the detecting signal photons from our method, which agrees well with the results (15.56 m) from the GFCH (Global Forest Canopy Height) dataset. Overall, for different land cover types in coastal areas, our study indicates that the proposed method can significantly improve the performance of the signal photon detection for photon-counting lidar data, and the detected signal photons can further obtain the water levels and vegetation heights. The proposed approach can also be extended for ICESat-2 (Ice, Cloud, and land Elevation Satellite-2) datasets in the future. [ABSTRACT FROM AUTHOR]