Increasing problems in and pressures on coastal zones and subsequent high-ranking political initiatives to deal with these problems have resulted in several efforts to measure state of and progress towards sustainability in coastal zones. The project SUSTAIN developed an indicator-based methodology and scoring system which allows municipalities as well as district and regional authorities to evaluate their sustainability performance. The results shall serve as a policy and strategic planning tool and improve the management of coastal zones. Ten groups applied the indicator set in two contrasting Baltic coastal municipalities, Neringa in Lithuania and Warnemünde in Germany. Nine groups were composed of five students, and the tenth group had a single expert. The variability of results from different groups is high for both study sites and on every data aggregation level. The data's limited reliability and reproducibility hinders regional, national and European inter-comparisons between sites. Indicator applications for time series are also problematic due to limited data availability, quality, and spatial resolution, as well as shortcomings in the indicator set and the human factor. The role of evaluators and their background and spatial heterogeneity are discussed, and recommendations are given. Overall, the interactive application process supports a learning-focused process for building awareness of sustainability and favours strategic planning. In combination with the QualityCoast labelling system, the SUSTAIN methodology can provide convincing practical benefits for municipalities