A regional cross-calibration between the first Delay–Doppler altimetry dataset from CryoSat-2 and a retracked Envisat dataset is here presented, in order to test the benefits of the Delay–Doppler processing and to expand the Envisat time series in the coastal ocean. The Indonesian Seas are chosen for the calibration, since the availability of altimetry data in this region is particularly beneficial due to the lack of in situ measurements and its importance for global ocean circulation. The Envisat data in the region are retracked with the Adaptive Leading Edge Subwaveform (ALES) retracker, which has been previously validated and applied successfully to coastal sea level research. The study demonstrates that CryoSat-2 is able to decrease the 1-Hz noise of sea level estimations by 0.3 cm within 50 km of the coast, when compared to the ALES-reprocessed Envisat dataset. It also shows that Envisat can be confidently used for detailed oceanographic research after the orbit change of October 2010. Cross-calibration at the crossover points indicates that in the region of study a sea state bias correction equal to 5% of the significant wave height is an acceptable approximation for Delay–Doppler altimetry. The analysis of the joint sea level time series reveals the geographic extent of the semiannual signal caused by Kelvin waves during the monsoon transitions, the larger amplitudes of the annual signal due to the Java Coastal Current and the impact of the strong La Nina event of 2010 on rising sea level trends.