EU standardised methods
A broader understanding and commonly agreed methodological standards are needed to implement monitoring of D6 criteria. D6 monitoring parameters have been inventoried by Zampoukas et al. (2012):
The efforts to make these indicators broadly operational are driven by the ongoing revision but benefit as well from the standards and reports produced by other directives, policies and regional sea conventions. EU guidance is available in the following links:
Regional Seas Conventions standardised methods
The In-depth assessment (2014) showed that there is a very low integration between D6 implementation in the scope of the MSFD and the RSC development of similar criteria. This highlighted the existing gap in the development of agreed methods for the implementation of D6 at regional levels. 

Parallel work towards selecting and developing environmental status indicators under the different Regional Sea Conventions covering the EU waters is relevant for this process. 

The OSPAR Ecological Quality Objectives for threatened and/or declining habitats (EcoQOs) identifies 16 seabed habitats and associated communities which are threatened and/or declining and can contribute to the implementation of D6 of the MSFD. Six indicators pertaining to D6 are included in the developing under OSPAR list of common biodiversity indicators that relate either to seabed habitat quality or spatial extent of the damage from human activities. They include: BH1 Typical species composition, BH2 Multi-metric indices, BH3 Physical damage of predominant and special habitats, BH4 Area of habitat loss, BH5 Size-frequency distribution of bivalve or other sensitive/indicator species, and PH1 Changes of plankton functional types (life form) index ratio. They encompass several biodiversity components such as phytoplankton, zooplankton, angiosperms, macroalgae and benthic invertebrates. Not all of these indicators are operational yet.
HELCOM, through the CORESET II project, has developed a suite of indicators that are relevant for D6. Part of these indicators will form the core of the commonly agreed indicators among the HELCOM Contracting Parties but pre-core and candidate indicators are also considered. Both state and pressure indicators are under development. Five of the indicators are addressed at benthic habitats and communities. Furthermore, HELCOM has developed a Red List biotope classification which identifies threatened biotopes.
The implementation of the Barcelona Convention has established that Contracting Parties will gradually implement the Ecosystem Approach (EcAp) to the management of human activities in the Mediterranean. Indicators and monitoring programmes to support the 11 Ecological Objectives (EOs) of EcAp, including biodiversity objectives similar to those of MSFD, are currently under development. A list of habitats and species has been proposed for priority monitoring and assessment in relation to EO 1 (equivalent to MSFD D1). These are likely to influence also monitoring priorities under D6, since this RSC is trying to establish some compromise between EU MS MSFD minimum obligations and the objectives of non-EU contracting parties. Biodiversity Descriptors, EO 6 included, are being discussed in view of EO 3 (i.e., MSFD D3) in order to address links between fisheries and biodiversity monitoring needs.
The Black Sea Strategic Action Plan (2009) provides a list of Ecosystem Quality Objectives (EcoQOs) towards achieving the overall long-term desired ecosystem state of the Black Sea. The physical loss and damage of the sea floor have not been among the prioritised environmental problems in the Black Sea region but dredging and disposal of dredged material have received some attention. A number of management targets related to water pollution with hazardous substances may also contribute to seafloor integrity sensu lato. Indicators to assess the different EcoQO have been listed at three levels: process, stress reduction and environmental status.