Non-indigenous species
The monitoring of non-indigenous species, as required by the MSFD, should allow for the protection of marine ecosystems from their adverse effects on environmental quality resulting from changes in biological, chemical and physical properties of aquatic ecosystems. 

Non-indigenous species do not respond in the same way as a chemical pollution or eutrophication which may be diminished provided that appropriate measures are taken. The risk of new biological invasions can be most effectively reduced by precautionary measures (e.g. ballast water management); while control or eradication of existing IAS is more challenging. NIS may expand their distribution and increase their abundance from a local source through processes which may not be controllable. The spatial extent, rate of spread and impacts on the environment will depend on biological traits of a NIS and environmental conditions within an invaded ecosystem.

A review of D2 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 11 to 12)
Technical work is ongoing to establish an operational MSFD Methodological Standards framework for D2 (e.g., under WG GES).
Additionally, the DEVOTES FP7 project has recently developed a software tool to help selecting indicators for the MSFD: the Devotool. Among the list of scientific indicators compiled, several are potentially useful to assess environmental status under D2. This resource can be used as an additional source of information to help establishing methodological.
Pollution effects on the ecosystem components
Biological pollution is the impact of IAS at a level that disturbs environmental quality by effects on: an individual (internal biological pollution by parasites or pathogens), a population, a community, a habitat or an ecosystem. 

The impact assessment needs to be coherent with Descriptor 1 and other relevant policies it is necessary to establish how to define GES in cases when the impact on ecosystem as a whole apparently is minimal but e.g. there is a strong impact on e.g. a protected species.
Threshold values
The establishment of a baseline information is required for the assessment of trends in new introductions, and the agreement on the principle for setting the baseline is essential for the coherent assessment of the particular indicator within and across marine regions. Without a standardized monitoring frame and a quantitative baseline, setting thresholds is not scientifically and statistically relevant In conclusion. An interim "goal" of a declining trend in new introductions. 

Measuring the impact of invasive NIS is difficult and that there are not enough scientific data or monitoring programmes to support this assessments. The Biological Pollution Index (BPL) used by some Member States, but evaluated as not relevant by some others, is not generally accepted.