According to WFD, European countries shall establish monitoring programmes for water quality overview. In EcoSUSTAIN, an Interreg–MED project, Gap analysis, an approach that reveals the difference between current and desired level, was carried out, targeting five Mediterranean hydro-ecosystems covering “Monitoring Practices” and “Water Quality and Pressures”. Our goal is to investigate practicing deficiencies, as long as information lack and distance from desirable status, supporting water uses and WFD goals. Data was collected by literature research supported by questionnaires. The findings on both fields, revealed problematic areas dealing with the compliance with the WFD and several deficiencies in tackling pressures.