This topic investigates in more detail the possible links between biodiversity, ecosystem functions and services dimensions of the AQUACROSS Assessment Framework. Using the outcomes of the Assessment Framework, this topic develops guidance on the application of indicators and methods to further understand causalities in the case studies. The suitability of the proposed indicators and methods for the assessment in the case studies are investigated and proposals to improve the Assessment Framework are made. The results coming from the case study assessment are used to provide policy recommendations on the practical application of the Assessment Framework on the case studies.