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The European Biodiversity Strategy asks EU Member States for an assessment, mapping and valuing of Ecosystem Services (ES). While terrestrial ES concept is advanced and different tools are available, they are largely lacking for coastal and marine systems. We develop a stepwise methodological process to assess ES in coastal and marine systems which we name Marine Ecosystem Services Assessment Tool. We applied it to two large Baltic lagoons, the Szczecin and the Curonian Lagoons demonstrating a quantitative and qualitative assessment approach. Firstly, an initial status is defined reflecting, according to the European Water Framework Directive, a past situation when the ecosystems where in a so called good ecological state. In both Baltic lagoons, this refers to a situation around 1960. Secondly, a present state is defined, assessed and compared to the initial status. Increasing anthropogenic impacts in Szczecin Lagoon caused an overall decrease ecological status which may influence the system's ability to provide services. Assessing ES changes semi-quantitatively via 39 indicators and 22 services, we show a decrease in provisioning and regulating and maintenance and an increase of cultural services' provision. According to 15 expert valuations, the Curonian Lagoon displays no changes in provisioning but an increase in regulating and maintenance and cultural service provision. We discuss how these results can serve different marine management approaches and support different polices. Through our application we show how the tool can be used to assess ES changes over time and thus provide key information on sustainable use and ES for future generations.