The marine environment provides resources such as fish, seafood, water for desalination, and supports key sectors such as transport (of goods and people), tourism, recreation, energy, and telecommunications. The sea plays a key role and is important for everyday life and for the economy.

Inland and transitional waters are likewise valuable landscape features and support biodiversity in important natural areas, which are also appreciated by the residents and tourists for various recreational activities.

Human activities, if not well managed, can exert pressures on aquatic ecosystems and eventually lead to a deterioration in the status of these waters, with knock-on effects for the very services that these ecosystems provide. Examples of such pressures include the following:

  • Water pollution can occur from the introduction of various substances – natural or synthetic – including nutrients, suspended matter, bacteria and viruses, heavy metals, pesticides, and other synthetic chemicals. There are various sources of such pollution including agriculture, industry, urban wastewater, and shipping, and can be diffuse or point sources. Pollution can result in a decrease in light and oxygen availability, accumulation of particulate wastes, increased stress to aquatic life, alteration of habitats, and possible increased mortality in aquatic organisms.
  • Littering detracts from the visual appeal and amenity of natural areas, poses a risk to the animals that live in or visit the area – as these can become trapped in the discarded items or ingest them – and contaminates the environment as it degrades, releasing toxic substances or breaking down to microplastics that persist in the environment and enter the food chain.
  • Noise and light pollution from human activities can disturb aquatic fauna – especially seabirds and cetaceans – that use these areas for rest, breeding or foraging for food, disrupting their natural behaviour and in some cases resulting also in mortality.
  • Activities that take resources from the sea, such as fishing – be it professional or recreational – has the potential to upset the ecosystem, lead to declines in populations of aquatic animals, also through direct unintended mortality (incidental by-catch). Incidental by-catch can be of particular signficance when the fish and other aquatic animals that are caught are already endangered due to low population abundance or are protected. Seabirds and turtles can also be injured or killed as ‘by-catch’ when they are caught in fishing gears.
  • Damage to seabed habitats and the animals that live in them can result from construction at sea, as well as activities such as dredging, which can obliterate habitats, lead to the resuspension of sediments that can then smother fauna and flora, or change the water currents which in turn can impact ecosystems in the area.
  • Vessels can also lead to environmental damage, such as from anchors dragging on seagrass meadows and reefs. Recreational activities such as diving and snorkelling can also cause disturbance: touching cave walls and reefs can disturb the fragile sponges and other organisms that live on them.


In order to manage activities, and the pressures that these are exerting on aquatic ecosystems, we need to understand what the status of our waters is, whether they are being impacted and if so, by which activities, in what ways and to what extent. The significance of these impacts can then be used to guide management efforts.

The status of Malta’s surface waters is assessed in line with the Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD).

The WFD seeks to implement an integrated approach and establish a framework for the protection of inland surface waters, transitional waters, coastal waters and groundwater. Under the WFD, the status of water bodies is assessed on the basis of various physical, chemical and biological elements, every six years and the assessment is published in Malta’s Water Catchment Management Plan.

The MSFD complements and extends the scope of the WFD, both geographically and in terms of the elements – or ‘descriptors’ – that need to be assessed, and which consider pressures on the marine environment as well effects on biological diversity. In addition, the characteristics that shall be used to assess ‘Good Environmental Status’ must be defined and Environmental Targets set. The assessment under MSFD is undertaken every six years and is published as Malta’s Assessment Report under Articles 8, 9 and 10 of the MSFD.

These assessments are carried out on the basis of monitoring data as well as information on various activities that are carried out in our waters.


Management measures that are needed in order to either achieve or maintain our waters is a good state are developed on the basis of the assessments carried out, and target gaps or issues that have been identified.

The Water Catchment Management Plan includes the programme of measures that is necessary for good status to be achieved in Malta’s waters in line with the WFD. These include ‘basic’ measures that are required under other legislation, such as the Urban Wastewater Directive and the IPPC Directive, as well as additional measures – called ‘supplementary measures’ – that are required to address the Significant Water Management Issues identified as part of the assessment process.

The MSFD likewise requires the development of a programme of measures to achieve or maintain good environmental status in all marine waters under Malta’s jurisdicational rights, on the basis of the assessment carried out and the environmental targets that have been set.

The Water Catchment Management Plan and the MSFD Programme of Measures are updated and published every six years.

The measures also take into consideration the conservation measures that are required to achieve the site-specific conservation objectives of the marine Natura 2000 sites, to ensure that a coordinated and consistent approach is taken to Malta’s management of its marine waters.  While the WCMP and MSFD Programme of Measures provide an overarching framework for management at a National scale, site-specific management measures are also developed for Natura 2000 sites covering aquatic ecosystems, thus ensuring a holistic framework of complementary actions targeting the protection of such ecosystems at different scales.

The programme of measures developed under the WFD and MSFD are drafted in close collaboration with all relevant stakeholders and are subject to public consultation. The two Directives integrate economics into water management and policy making and call, either implicitly or explicitly, for economic analyses under various provisions. The economic requirements and objectives of the two Directives include amongst others:

  • an analysis of water uses in terms of their economic value, and (under the MSFD) an assessment of the costs of degradation of marine waters;
  • the establishment of objectives and targets with due consideration of social and economic concerns;
  • the assessment of the social and economic impacts of the management measures and cost-effectiveness analyses of such measures

The costs of the measures also need to be estimated and included in the published documents.