Due to the large variety of seafloor types, it is necessary to define indicators and standardized methods that can effectively convey the status of benthic ecosystems (i.e. those associated to the sea-floor) and of their alteration by pressures from human activities. 
A review of D6 methodological standards available through EU Directives, Regional Sea Conventions and ISO standards for the first MSFD cycle can be found in Piha & Zampoukas 2011 (pages 27 to 30)
Methods used in assessing GES under the WFD can also be often used in assessing GEnS under the MSFD.

Technical work is ongoing to establish a comprehensive and operational MSFD Methodological Standards framework for D6 (e.g., under WG GES).
Additionally, the DEVOTES FP7 project developed a software tool to help selecting indicators for the MSFD: the Devotool. This resource can be used as an additional source of information to help establishing methodological standards.
Human activities induce different kinds of pressures that can affect the sea-floor. The main pressures that directly impact the state of the sea bottom are:
  • Coastal infrastructures (ports, defences against erosion, etc.) and offshore installations (oil and gas platforms, wind farms, etc.)
  • Offshore mining and sand extraction
  • Release of dredged sludge
  • Moorings
  • Some fishing practices (trawling, dredging, etc.)
  • Aquaculture (unused fish feed, fish faeces, etc.)
  • Introduction of non-indigenous species (trough ballast water for instance)
  • Pollution (chemical pollution, litter)
  • Changes in riverine inputs (organic enrichment of particulate matter, etc.)
  • Sediment remobilization by fishing equipment (trawls, dredges)
  • Changes in freshwater riverine inputs as a consequence of damming and irrigation
  • Changes in solid matter riverine inputs and
  • Release of large quantities of warm (power plant cooling) or salty water (from desalination facilities)
The mapping and quantification of the pressures applied to the sea-floor is an essential part of assessing and monitoring its ecological status. Data of the distribution of human activities must be collated to estimate, for example, the proportion of the seabed significantly affected by human activities for the different substrate types.
The pressures listed above, acting in isolation or together, may impact the structure of benthic ecosystems. For instance, changes in species composition may be induced by the damage of large or fragile species or by changes in their functioning. Others may be associated to the stimulation of opportunistic or scavenging species that may profit from disturbance of the bottom and availability of dead organisms. 

Indicators concerning the state of the benthic ecosystems need to be based on the presence of particularly sensitive or tolerant species or habitats. More robustly, they can be indices calculated from several parameters such as the species diversity, species richness and the proportion of different species groups in benthic samples. 

A particular attention has to be paid to some remarkable habitats that, in spite of their reduced spatial extent, play an important role in marine ecosystems dynamics and biodiversity (e.g. biogenic reefs, cold-water corals, maerl beds). The distribution of these and other habitats may be mapped from geo-referenced data gathered by acoustic sonars and optical camera surveys. Repeated surveys are only practicable for some particular habitats distributed over small/discrete areas but they are fundamental to gather information on possible changes in habitat extent.