The following tables give an overview of the main threats affecting different habitat types known from the Maltese Islands.
| Terrestrial Habitats | Examples of Threats |
| Garrigue | Land reclamation Fly-tipping Land conversion, degradation, fragmentation and loss Quarrying activity Invasion by non-native species Over-grazing Intentional fires Clearing of vegetation Littering |
| Saline Marshlands | Land conversion, degradation, fragmentation and loss Dumping of building waste and domestic refuse Invasions by weed species Vandalistic acts |
| Coastal Wetlands | Rubbish dumping Trampling |
| Freshwater Rock Pools | Habitat loss |
| Sand Dunes | Land conversion and inappropriate land use Trampling, dumping, fire and other disturbances resulting from human activity Impact of non-native species Natural disasters, such as storms |
| Valley Watercourses | Land conversion Dumping of building waste and domestic refuse Nutrient over-enrichment via run-off of nitrates/phosphates from farmed land Invasion by non-native species Diversion of water from watercourses |
| Rupestral Habitats | Quarrying activity |
| Marine Habitats | Examples of Threats |
| Supralittoral/Mediolittoral Rock | Loss of habitat by coastal land-use change Dumping of building waste and littering Land pollution Effluent run-off |
| Supralittoral Sand | Trampling Romval of sand Mechanical damage |
| Posidonia Banquettes | Removal of drying and decaying plant debris on beaches |
| Seagrass meadows | Mechanical damage Activities that result in habitat loss and degradation Pollution Increase in water turbidity Terrestrial run-off of effluents (including from agricultural practices) Invasion by non-native species (such as Caulerpa racemosa) Bottom trawling Anchoring Dredging works Thermal effluents Deleterious effects that may arise from fish farm and tuna pens |
| Cystosiera Communities | Organic pollution Dumping Fishing Changes in sedimentation/current regime due to developments |
| Cladocora caespitosa Banks | Over-collecting Pollution Mechnical damage by anchors and fishing gear Smothering by sedimentation from development |
| Coralligene Communities | Bottom trawling Dumping Changes in sedimentation regime due to land-use change |
| Maerl Communities | Bottom trawling Possible dumping Pollution Invasion by non-native species |
Other sections related to habitats
Habitats
Terrestrial Habitats
Marine Habitats
Habitats Fragmentation & Edge Effects Links for further information
State of the Environment Reports / Indicators
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