Description of Activities


The monitoring processes of selected themes and related assessment were carried out through Service Contract CT 3031/2016, with the aim of ensuring long-term feasibility of the monitoring processes.

The monitoring data was then analysed, the environmental status assessed and environmental targets proposed with a view to bridge monitoring data with management regimes.

The themes covered through this contract were the following:


Water Column Habitats

Water column habitats are generally referred to as “pelagic” habitats, and include the water column and all the organisms that inhabit it. Monitoring of such habitats focused on the composition, abundance and biomass of communities of phytoplankton and zooplankton, which are microscopic organisms which form the base of food chains within the water column and are therefore key indicators of the condition and health status of this habitat. Physiochemical and hydrological parameters were also monitored.

Seabed Habitats

Seabed, or benthic, habitats are defined based on the physical substrate, hydrological characteristics such as temperature, salinity and water movement, and the composition of species communities associated with the seabed, as well as species present.

The project monitored selected seabed habitats such as macroalgae along the coastline, seagrass beds and maerl beds, to assess their extent and condition, through the assessment of benthic species living in the sediments.

Non-Indigenous Species

Non-indigenous species are also known as alien species; species that have been introduced outside of their natural range and their natural dispersal potential, intentionally or unintentionally as a result of human activities. These species may threaten or adversely impact local biodiversity and related ecosystem services.

The project monitored the occurrence of non-indigenous species in Maltese Marine Protected Areas (MPAs) and hotspots, while also providing an indication of the abundance of selected species groups, including phytoplankton and zooplankton communities in the water column habitats. This monitoring enabled an assessment of the pressures arising from non-indigenous species in Maltese waters and will identify appropriate management measures to be taken.


Increased levels of certain nutrients in the marine environment, generally nitrogen and phosphorus, can lead to enhanced primary or biomass production. This can result in reduced light penetration in the marine environment and increased carbon fixation, resulting in algal blooms, and changes to the taxonomic composition of algae and plants. The consequences of this process, called eutrophication, are undesirable since they can degrade ecosystem health and/or the sustainable provision of goods and services, apart from being visually unattractive. Increased levels of organic matter in the marine environment are also associated with negative effects on the marine environment.

The project monitored nutrient levels in the water column and organic matter in the sediment, as well as the effects of eutrophication through links with other monitoring processes.

Hydrographical Changes

The physical parameters of seawater – temperature, salinity, depth, currents, waves, turbulence and turbidity – change as a result of large scale human activities, such as coastal defence works and structures in coastal or open sea which can permanently influence the hydrographical regime of currents, waves and sediments. These changes can in turn induce further changes to sediment transportation, seabed structure, salinity and temperature which might lead to effects on marine ecosystems as a result of changes to their immediate dynamic environment or through food chain effects.

In addition to the physical characteristics of the water column, the project also included spot measurements of current profiles. The data collected will feed into hydrographical models that will be developed through other EU funded projects with the aim to learn more about the baseline conditions of Maltese waters, thereby enabling the monitoring of these baseline conditions.


Contaminants or hazardous substances are defined as chemical elements and compounds or groups of substances that are toxic, persistent and liable to bioaccumulate, and other substances or groups of substances which give rise to an equivalent level of concern.

Hazardous substances can be broadly classified into two principal groups: synthetic substances and non-synthetic substances. Synthetic substances refer to compounds such as pesticides, pharmaceuticals and anti-fouling agents; whereas non-synthetic substances include naturally occurring substances such as trace metals, aliphatic and aromatic hydrocarbons, as well as by-products of combustion activities.

Through this project, a selection of contaminants listed in the Priority Substances Directive 2013/39/EC as well as other contaminants of national concern, were monitored in water, sediments or biota.

Marine Litter

Marine litter is defined as ‘any persistent, manufactured or processed solid material discarded, disposed of or abandoned in the marine and coastal environment’. Based on this definition therefore, marine litter consists of items made or used by people, such as plastics, wood, metals, glass, rubber, clothing and paper, discarded in the sea and on beaches, deliberately or unintentionally.

This project monitored the characteristics and abundance of the marine litter which is present in the water column and on the seabed, as well as marine litter washed ashore.

The monitoring programmes for these themes were first updated on the basis of the data collected, so as to address any shortcomings in the established monitoring procedures and increase the efficiency of the project’s monitoring efforts. The implementation of the monitoring processes was subsequently initiated in July 2017 and completed in March 2019.

The data collected as part of this service contract was analysed on the basis of established criteria and indicators. This analysis is presented in an assessment report which fed directly into the update of the environmental status of Malta’s marine waters as reported for the purposes of the Marine Strategy Framework Directive.

The assessment of status is based on criteria and indicators, and associated thresholds established by processes or guidance documents pertaining to the EC Habitats Directive (92/43/EEC), the Water Framework Directive (2000/60/EC), the Marine Strategy Framework Directive (2008/56/EC), and the newly revised Commission Decision 2017/848, and works towards streamlining the status definitions across these documents.

A robust database system from which marine related datasets can be extracted was produced through the project. The database facilitates access to relevant information, allowing the public to understand the status of the marine environment and follow the country’s progress towards the achievement of good status. The datasets for QGIS​ can be accessed from here.​​​


There are a few confirmed species of marine mammals (or cetaceans) that regularly occur in Maltese waters. These include the bottlenose dolphin (Tursiops truncatus), the common dolphin (Delphinus delphis) and the striped dolphin (Stenella coeruleoalba). Other cetacean species which are occasionally sighted include the Risso’s dolphin (Grampus griseus), the fin whale (Balaenoptera physalus), the Cuvier’s Beaked whale (Ziphius cavirostris) and the sperm whale (Physeter macrocephalus). 

Striped dolphin
Striped dolphin

Marine reptiles on the other hand are represented by one species in Maltese waters: the loggerhead turtle (Caretta caretta).

Three Marine Protected Areas have been designated for the conservation of Tursiops truncatus and Caretta caretta in Malta’s Fisheries Management Zone (MT0000113, MT0000115 and MT0000116), which areas were adopted as Natura 2000 sites in accordance with the EU Habitats Directive 92/43/EEC. The designation of these Marine Protected Areas was based on systematic surveys carried out through the LIFE+ MIGRATE project in the summers of 2013 and 2014.

Loggerhead turtle in water
Loggerhead turtle

The EMFF project sought to update monitoring processes for marine mammals and marine reptiles in Maltese waters, as well as test these processes on a pilot scale, with the aim to substantiate previous data and achieving long-term monitoring processes as required by the EU Marine Strategy Framework Directive (2008/56/EC) and Habitats Directive (92/43/EEC).

Experts’ assistance was sought through a separate procurement process under this project (GF/Admin/40/2020). The related monitoring activities, which included aerial and boat-based surveys were implemented in summer 2021.

Researcher listening to hydrophone
Researcher listening to hydrophone

A rehabilitated turtle Chopsly was also equipped with a satellite tag for tracking its vertical and horizontal movements following its release, which took place on 23rd August 2021. Although the signal was lost shortly after the turtle was released, insights on the importance of tracking in turtle monitoring to understand patterns in behaviour, spatial habitat use and the turtle’s use of the water column, were obtained nonetheless.

Chopsly being released
Chopsly being released

The contract delivered a Data Analysis Report and Long-term Monitoring Strategy, to guide future monitoring efforts.

A form to submit sightings of marine mammals and turtles has been developed, for use by the public. This is available online and will continue to be used post-project.

Pod of dolphins near boat
Pod of dolphins near boat

Malta is considered to be an internationally important breeding location for three seabird species, Scopoli’s Shearwater (Calonectris diomedea), Yelkouan Shearwater (Puffinus yelkouan) and the European Storm-petrel (Hydrobates pelagicus). The coastal cliffs and screes, which predominate along the southwestern coast of the archipelago provide shelter and a breeding habitat to these seabirds.

Scopoli's shearwater
Scopoli’s shearwater

Data used for assessment and conservation of these species has to date been primarily collected by independent researchers and through EU funded projects led by BirdLife Malta in particular the LIFE+ Malta Seabird Project (LIFE10 NAT/MT/090 – 2011-2016) and the LIFE Archipelagu Garnija Project (LIFE14 NAT/MT/000991 – 2015-2020). A continuous data collection process for these seabirds however needs to be ensured to enable assessment of trends and the conservation status of these species in accordance with the requirements of the EU Marine Strategy Framework Directive and the EU Birds Directive.


Storm petrel with egg
Storm petrel with egg

This project sought to address the MSFD and Birds Directive requirements by developing and implementing a monitoring strategy for seabirds in Malta, building on Malta’s MSFD monitoring programme and involving the use of alternative monitoring methodologies. On the basis of the implementation of this monitoring strategy on a pilot basis in 2021, a Long-term Monitoring Strategy was developed that can be adopted by Malta as part of the marine monitoring programme for the continuous assessment of status.

Measuring beak of Scopoli's shearwater
Measuring beak of Scopoli’s shearwater

Experts’ assistance was sought through a separate procurement process under this project (GF/ Admin/48/2020). The fieldwork, which included a variety of methods to cater for the different colony sites, was carried out during part of the 2021 breeding period (April – July/August), as described in the Fieldwork Report. A Long-term Monitoring Strategy was then developed, to guide future monitoring efforts.

Ringing European Storm petrel
Ringing European Storm petrel

Marine food webs refer to networks of marine organisms linked by feeding interactions. The exchanges of energy and nutrients through the food chain reflect the functioning of ecosystems. Anthropogenic activities can cause changes to the structure and dynamics of the food webs, thus affecting ecosystems as a whole.


The EU Marine Strategy Framework Directive 2008/56/EC (MSFD) addresses ecosystem aspects through food webs by dividing the structure and function of food webs into compartments which share common features, i.e. ‘trophic guilds’. Trophic guilds may refer to important prey groups (defined by who eats them) as well as predators (a group that eats the same thing).


This project sought to establish a monitoring protocol for trophic guilds in Maltese waters through the identification of indicator species and collection of data in consideration of existing monitoring processes for the purpose of establishing long-term cost-effective monitoring processes in line with the requirements of the EU Marine Strategy Framework Directive (2008/56/EC).

Slipper lobster
Slipper lobster

This work was implemented through a separate procurement process (SPD8/2021/016), through which a Monitoring Strategy and Pilot Implementation Report were produced. The aim of this work is to enable the long-term monitoring of ecosystems and shed light on their status, thus contributing to better implementation of ‘an ecosystem-based approach’ to management.

A series of communication events and tools aimed at disseminating information on the outcome of the project were carried out through contract CT 3031/2016. These included four stakeholder seminars, a closing conference, features on radio and TV programmes as well as press releases issued throughout the project duration.

First Stakeholder Seminar: 6th April 2018

The main objectives of this session was to:
• Introduce the project and its main objectives
• Outline the progress of the project and some preliminary results
• Describe the proposed database and its purpose
• Invite comments from the attendees relating to the project components


Second Stakeholder Seminar: 5th October 2018

The main objectives of this session was to:
• Provide an introduction and overview of the progress achieved
• Describe the data collected in the first year
• Outline the recommendations made in the update of the monitoring programme
• Describe the plan for the second year of monitoring

Third Stakeholder Seminar: 11th December 2018

The main objectives of this session was to:
• Provide an introduction and overview of the progress achieved
• Describe the data collected
• Give an overview of the database and its relevant applications

Fourth Stakeholder Seminar: 27th February 2019

The main objectives of this session was to:
• Describe the results that were collected during the first and second monitoring year
• Provide the final steps of the project together with policy implementation and reporting matters

Closing conference

The final conference for CT 3031/2016 was held at Sala Antoine de Paul, San Anton Palace on the 29th May 2019 with a total of 54 attendees including representatives from the Environment and Resources Authority (ERA), Malta Marine Monitoring Consortium (M3C), the Ministry for Environment, Sustainable Development and Climate (MESDC), the Funds and Programs Division (FPD), the Planning Authority, the Department of Fisheries and Aquaculture, the Ministry for Transport, Infrastructure and Capital Projects (MTIP), the Malta Competition and Consumer Affairs Authority (MCCAA), Malta Marittima, Transport Malta, the Wild Birds Regulation Unit (WBRU), the Environmental Health Directorate (EHD), Ministry for Gozo (MGOZ), University of Malta, Continental Shelf Directorate and the general public.

The Minister for Environment, Sustainable Development and Climate Change, Dr. Jose Herrera, the Parliamentary Secretary for European Funds and Social Dialogue Dr Aaron Farrugia, Director of Environment & Resources, Perit Michelle Piccinino (ERA) and Ing Mario Schembri (M3C) gave introductory speeches.

The main deliverables of the project were discussed with the stakeholders and the general public. The conference also ended with break-out sessions related to the monitoring programme, status assessment and database use and applications.

In addition to the above, the additional projects following the closure of CT 3031/2016 will also seek the development of a promotional video targeting improvement of public awareness on the Integrated Maritime Policy.

In addition, a short video was developed, through a separate procurement process (CfQ: ERA_QT23/2021), to raise awareness on the Integrated Maritime Policy (IMP, the European Maritime and Fisheries Fund (EMFF) and the monitoring processes undertaken through the project.

Video in English
Video with English subtitles
Vidjo bil-Malti
Vidjo bis-sottotitoli bil-Malti