Nature Conservation

Main issues

Ecosystem-based approach and sustainable development are key principles of MSP, and require appropriate consideration of ecological implications throughout the MSP process, to ensure sustainable expansion of marine sectors. The MSFD is intended to provide a mechanism of ensuring ecological protection at an ecosystem scale, and is seen as a complementary pillar to MSP, to reconcile growth in marine activities with minimal negative impact on the marine environment.

Although the environment is a key consideration throughout planning, special attention is also required to those ecological features which are afforded specific protection under conservation legislation, including primarily the Habitats and Birds Directive (Council Directive 92/43/EEC). The Habitats Directive requires the protection of key species and habitats through a 2-pillar approach of designation of marine protected areas (MPAs) and specific measures addressing the species listed on Annex IV(a) of the Directive (see question “How are mobile species with conservation status considered in MSP?”).

As a defined spatial element of conservation, much emphasis is placed on the primary pillar, i.e. designation and inclusion of MPAs in planning processes in order to achieve conservation objectives. In most cases, MPAs have already been designated and are therefore incorporated into the MSP process when allocating areas for other activities (for example in Germany). Their status would not be expected to change through MSP, and the objectives of the MPA will be a consideration in planning activities which may interact with the site or its’ conservation features. Where MPAs are established MSP can support their designation and understanding of objectives in relation to other interests.  In any case, it is important to note the great variety of types of different MPAs as recognised by IUCN’s 7 different categories [1] of protection, and that all may need to be considered within developing MSP. In fact, different synergies can be identified between the various MPA categories and the other maritime sectors.

[1] Dudley, N. (Editor) (2008). Guidelines for Applying Protected Area Management Categories. Gland, Switzerland: IUCN. x + 86pp. WITH Stolton, S., P. Shadie and N. Dudley (2013). IUCN WCPA Best Practice Guidance on Recognising Protected Areas and Assigning Management Categories and Governance Types, Best Practice Protected Area Guidelines Series No. 21, Gland, Switzerland: IUCN. Available at

Please note that this section of the EU MSP Platform website is not currently being updated with new information. However, the resources throughout our website remain relevant to our mission of sharing knowledge and experiences on MSP in the EU.

Frequently Asked Questions

A multi-criteria assessment framework, integrating environmental accounting with MSP, can be pursued to allow a broad and interdisciplinary approach to nature conservation and spatial planning. This approach was applied to the case of the Egadi islands (Italy)  where the biophysical and non-market monetary value of natural capital was assessed through the emergy accounting method. In addition, by using the Marxan software, the results of the environmental accounting were integrated with spatial data on main human uses to identify key areas for natural capital conservation, taking into consideration the trade-offs between protection measures and human exploitation.

From an operational point of view, the combined use of the Marxan software and a cumulative impact decision support tool can help to analyse areas suitable for conservation measures. This has been applied to the MSP process in Portugal, focusing on marine waters off the mainland of Portugal . For practical applications, the Cumulative Impact Model, developed by Fernandez et al. (2017)[1] would need to be adapted to a different context in order to be used as a surrogate for ecological condition, input as “costs” in Marxan.


[1] Fernandes M., Esteves T. C., Oliveira E. R., Alves F. L., 2017. How does the cumulative impacts approach support Maritime Spatial Planning?,Ecological Indicators 73: 189-202.

The objective of networks of MPAs are that they are ‘ecologically coherent’ which is fundamental to understanding the contribution of MPAs to an ecosystem-based approach, but ‘ecological coherence’ is a challenging concept to define and evaluate. Most definitions envisage MPA networks that maintain ecosystem processes, functions and structures and where individual MPAs function synergistically with others in the network. Criteria used to judge ecological coherence include representativity, replication, adequacy, viability and connectivity.

Understanding ecological functioning is a critical basis for ecosystem-based MSP, hence knowledge and analysis of such systems would be beneficial to developing a shared understanding of the system and the effects of proposed activities. Relating ecosystem functioning from a conservation perspective to the ecosystem services framework would improve communication of the potential for maritime activities to negatively affect ecosystem processes, functions and structures in MSP. It would also build understanding of the reliance of such activities on healthy ecological networks (in terms of benefits and services) such as fisheries and sustainable tourism.

Essential Fish Habitats (EFH) (those waters and substrates necessary to fish for spawning, breeding, feeding or growth to maturity[1]) and fish migration patterns can be used to assess the ecological coherence of Marine Protected Areas (MPAs) and eventually plan additional MPAs. In the BALANCE project, analyses of ecological coherence of the Natura 2000 network in relation to EFHs  was performed using existing maps of designated Natura 2000 sites, and maps of Natura 2000 habitat types. For a preliminary assessment of how well Natura 2000 habitat types may be representative of potential EFHs, the expected association of different fish species with defined Natura 2000 habitat types was estimated. Explicit analyses of connectivity and other aspects of ecological coherence (for example representativity) may be performed based on those fish species and life stages for which maps of potential EFH are currently available. This indirect approach can be used for broad, preliminary descriptions of the distribution of EFHs, but should be replaced by maps based on statistical models as soon as enough information is available for predictive modelling.


[1] U.S. Magnuson-Stevens Fishery Conservation and Management Act (1998)

In the second pillar of the Habitats Directive, animal species listed on Annex IV(a) present a further aspect for consideration, particularly as this includes the majority of mobile species (all marine mammals and many seabird species). Where possible, the areas of high sensitivity for such species should be represented spatially for inclusion within MSP mapping processes; for example, migratory bird routes or marine mammal foraging areas. However, data is often limited in being able to specifically define these, hence MSP processes would need to consider the potential for these to occur and enable subsequent planning to account for them.

Given the migratory nature and extensive range of these species, trans-boundary co-operation is necessary to manage issues at an appropriate scale in order to understand effects at a population level (a key determinant in evaluating the ‘significance’ of particular effects under the Habitats Directive). In this context, initiatives such as the Trilateral Wadden Sea Plan, reviewed through the ARTWEI project, addressing transboundary policy and management of the Wadden Sea are a fundamental starting point, since they enable development of a shared vision for a healthy environment and set the basis for co-operation in addressing shared ecological challenges.

MPAs generally do not mean exclusion of all marine activities. Depending on the features for which the sites are designated, the conservation status and conservation objectives for the site (i.e. are they in good condition? Is the aim to maintain condition or improve?), and the likely interactions between activities, the management measures for the MPAs will state what restrictions on particular activities are appropriate. This may include seasonal restrictions only (e.g. seal haul-out sites), or restrictions on certain activities (e.g. bottom-trawling in areas of sensitive seafloor habitats). The risk of adverse effect of proposed activities on a particular feature or site is therefore of critical interest, and will be location specific.

Reference documents exist which support understanding around environmental implications of proposed activities in an MSP context, including through the PartiSEApate project, which hosted a number of cross-sectoral workshops between sea users, including addressing environmental issues.

Given the likelihood of compatibility between marine activities and MPAs, a zoning approach to inclusion of MPAs in MSPs is therefore not always relevant (or at least not the only relevant one), as activities may overlap, in space and time, and innovative models of management may be appropriate, including seasonal controls on activities or promoting co-location of activities which promote and enhance environmental features, (e.g. sustainable tourism, artificial reefs at wind farm sites, etc.). Guidelines and regulation for the spatial and temporal management of marine activities must be therefore integral part of the MSP approach, in particular when dealing with MPAs,

Please note that this question is answered in detail on the following pages under MSP Sectors:

As experienced within the PlanCoast project in the Wismar Bay case (Germany), conflicts between tourism and nature protection can be solved through a process of spatial and seasonal differentiation. In fact, zoning for spatial and seasonal differentiation allows for flexibility and can be coupled with other forms of resource management. This is particularly important where ecological resources are concerned. Reserve areas or human activities may need to be shifted, limited or adapted. Use demands from commercial sectors should be as focussed as possible, in order to limit the impacts caused by undifferentiated demands.

Spatial and seasonal restrictions and other solutions to conflicts between nature conservation and commercial uses can be reached through voluntary agreements, a powerful tool that represent a practical, operational alternative to the formal process of creating a new protected site (very long and complex process). In the Greifswalder Bodden case - also within the PlanCoast project - the German WWF facilitated dialogue between nature conservation NGOs, the state Ministry for the Environment, and a wide range of local user groups and associations. Actual negotiations then took five years, with the last agreement signed in 2005.

In the planning process for the Gulf of Gdańsk (Poland), separate planning of areas with a specific environmental protection need was adopted in order to link to MPAs issue. Since the plan covers environmentally valuable areas subject to many economic pressures, it was decided that the whole planned area should be divided into smaller sea areas (basins) in order to properly reflect their specificities. The maritime spatial plan covering West Part of the Gulf of Gdańsk (pilot plan) has to consider some MPAs located adjacent to the densely populated terrestrial areas and thus subject to numerous pressures. Ecological considerations strongly influenced the definition of objectives for the Plan. The inclusion of ecologically valuable areas into the plan was done in three steps. First, an inventory of ecological value was carried out. Second, the types of human activity that might pose a threat to that value were assessed. Third, this knowledge was translated into concrete provisions and solutions within the plan.

Zoning is a spatial management tool particularly relevant to MPAs as it divides MPAs in different sub-areas where different activities are allowed or restricted with the aim to reduce competition for space among users (IUCN, 2004). MPA zoning usually include an internal no-take zone, where only minimal human activities are permitted (e.g. diving and swimming), a second surrounded area where more activities are permitted (e.g. diving and swimming as well as sailing with small boats, etc.), and a third surrounded area, where also fishing activities are allowed (European Commission, 2018). MPA zoning can effectively provide benefits to fisheries since the establishment of a no-take area can improve size, diversity, and abundance of fish stock in the surrounding areas (Spillover effect). Nonetheless, it should be noted that the size of the no-take zone as well as the fish species targeted and their level of mobility are all factors that influence the benefits generated by the establishment of a restricted area (European Commission, 2018). MPA zoning, if done by taking into account the different uses and by involving stakeholders in the design processes can minimise conflicts between different users and benefit biodiversity and fisheries by restoring fish stocks (Makino et al., 2013). Hence, MPA zoning can be indented as a valuable tool for conservation purposes.


European Commission (2018) Study on the Economic Benefits of MPAs and SPMs. Written by ICF Consulting Services Limited. Publications Office of the European Union: Luxemburg.
IUCN (2004) Managing Marine Protected Areas: A TOOLKIT for the Western Indian Ocean. IUCN Eastern African Regional Programme, Nairobi, Kenya, xii + 172pp.
Makino A, Klein CJ, Beger M, Jupiter SD, Possingham HP (2013) Incorporating Conservation Zone Effectiveness for Protecting Biodiversity in Marine Planning. PLoS ONE 8(11): e78986.

Pilot SEA for the Western Gulf of Gdansk

This practice illustrates how to prepare the SEA report for maritime spatial plans in line with the spirit of the SEA Directive when the planned area contains Natura 2000 sites.

Review of comprehensive management plan for Wadden Sea

The Trilateral Wadden Sea Plan is an agreement of how the countries envisage the coordination and integration of management of the Wadden Sea Area and of the projects and actions that must be carried out to achieve the commonly agreed targets. A joint vision was formulated that guides the implementation of plan.

Finnish Inventory Programme for the Underwater Marine Environment

The programme's (VELMU) objective is to survey marine habitats in Finnish waters, give an overview of species occurrence and develop a management system for data collected on the benthic marine environment. The programme collects data on the diversity of underwater marine biotopes and species.

Mapping of marine landscapes in the Baltic Sea

The BALANCE project outlined its approach of how the landscape of the Baltic Sea was mapped, including which seabed topographic, coastal physiographic and benthic data, secondary physical data as well as assemblages of species.

Mapping marine habitats in Kattegat

This pratical information set shows the mapping and modelling of habitats in the Kattegat.

Assessment of Ecological Coherence of the Marine Protected Areas Network

This set of practical information defines practical criteria and a first set of tools that can be used repeatedly to assess ecological coherence of the Baltic Sea MPA networks.

Representative Network of Marine Protected Areas (MPAs) in the Baltic Sea

This set of practical information presents a regional, systematic, transparent and ecologically based approach for identifying MPAs in the Baltic Sea.

Blue Corridors

This set of practical information introduces blue corridors and provides some examples and recommendations on how to work with Blue Corridors in practical marine spatial planning.

Mapping the marine landscape

This report summaries the work related to marine landscape and habitat mapping published in 17 independent BALANCE Interim Reports. The BALANCE mapping efforts has operated at two scales: regional sea and local/national.

Guide on available geo-data for coastal and marine planning

This guide shows which geo-data are available and indicates their characteristics as well as limitations. One finding was that there are more geodata available for marine areas than expected. Mostly these are mapped or modelled seabed and water characteristics, but there are also other kinds of data.

Guidance on sustainable aquaculture activities in the context of the Natura 2000 Network

The aim of this document is to offer guidance which would facilitate the knowledge and implementation of EU legislation underpinning Natura 2000 in relation to aquaculture activities. 

Marine Protected Areas in the Celtic Seas – Analysis of National Frameworks

The study analyses the national regulatory frameworks for MPAs in the Celtic Seas. It investigated the existing frameworks for marine conservation present in the Celtic Seas countries (France, Ireland and United Kingdom) and the differences between them. 


This document describes the results of the testing and proposing the operational measures for SSF governance and management in any MPAs located in the northern shore of the Mediterranean region.

Taking Marine Protected Areas into account in the context of Marine Spatial Planning

This study aims to provide an overview of the current state and potential marine protected areas within the area investigated in the SIMNORAT and SIMWESTMED projects, and their legal corresponding legal basis at a national and international legislation level. 

Marine Natura 2000 areas and Maritime Spatial Planning

This report examines and summarizes the role of the Natura 2000 nature protection framework in MSP. The report reviews the Natura 2000 framework from two perspectives 1) summarizing the Natura 2000 process at a general level for planning authorities: why, who, how and when to select, implement, manage and assess the Natura 2000 sites and 2) how the process interacts legally with MSP.

Cross border MPA Galicia bank – Vigo and Vasco da Gama seamounts

The Spanish and Portugese authorities discussed the idea to develop and manage and cross-border Marine Protected Area (MPA) between both countries. In order to achieve this, the case study presented in this report focused on the existing Spanish MPA of Galicia Bank and on the Vigo and Vasco da Gama Seamounts, located in the western limit of the geologic continental platform and on the northern limit of the Portuguese jurisdictional area.