Multimission satellite altimetry (e.g. ERS, Envisat, TOPEX/Poseidon, Jason) data have enabled a synoptic view of ocean variations in the past decades, including sea-level rise and mesoscale circulations. Since 2016, the Sentinel-3 mission has provided better spatial and temporal sampling compared with its predecessors. The Sentinel-3 Ku/C Radar Altimeter (SRAL) is one of the synthetic aperture radar altimeters (SAR Altimeter) which is more precise in coastal and lake observations. In this study, we validate Sentinel-3 Level-2 products in Baltic Sea coastal areas and two lakes in Estonia. Moreover, the Copernicus Marine Environment Monitoring Service (CMEMS) Level-3 sea-level anomaly data and the Nucleus for European Modelling of the Ocean (NEMO) reanalysis model outcomes are compared with measurements from a tide gauge network. A dense in situ water level network deployed along the coast for geodetic observation was utilised to provide ground truths for validating altimetry results. Three validation methods were used for Level-2 data: (i) collocated Sentinel-3 and GNSS ship measurements; (ii) a national geoid model (EST-GEOID2017) with sea-level anomaly correction; (iii) collocated Sentinel-3 and buoy measurements. The validations were carried out in seven Sentinel-3A/B overpasses in 2019. Our results show that the uncertainty of the Sentinel-3 Level-2 altimetry product is below decimetre level on the Estonian coast and the targeted lakes. Results from CMEMS Level-3 showed a correlation of 0.8 (RMSE 0.19 m) and 0.91 (RMSE 0.27 m) when compared against tide gauge measurements and NEMO model, respectively.