The biggest threat to aquatic plants in Europe is direct habitat loss; individual wetlands and parts or all of wetland complexes are still drained for development, agriculture or even pasture throughout the region. This is significant not only when it affects large wetlands and wetland complexes, but equally when it involves small superficially unimportant sites, such as seasonally inundated field corners, wet hollows in pasture and stock ponds. In the UK, for example pressure on land use has led to a general tidying up of the landscape, resulting in the loss of damp habitats in fields, seasonally wet tracks and ephemeral ponds, with a consequent decline in many species which were formerly abundant or are still abundant elsewhere.
Species which do not spend their whole life cycle within the water often depend upon fluctuating water levels to supress more aggressive taxa and stabilisation of water levels can eradicate entire populations of these species. Surface or groundwater abstraction can similarly have a significant adverse impact on aquatic plants, for example, Carex cretica, which is endemic to Crete, is threatened by the abstraction of water for irrigation. Abstraction of water from the ground, both for potable supply and agricultural use, is known to affect both the levels and the periodicity of fluctuation of water tables which in turn affect the timing and quantity of supply to natural springs and seepages upon which these wetland and river plants depend. The abstraction of water from rivers and lakes leads as well to ecological change with various consequences including the decrease of surface area of flooded wetlands and the duration of flooding. Rivers and other wetlands have been modified since humans first started to grow crops and keep livestock.
Most wetland types are naturally highly dynamic, resulting from natural processes at the ecosystem level. Many aquatic and wetland plant populations appear to function as dynamic metapopulations; these populations are linked by exchange of genetic material (e.g. pollen, propagules or even plant fragments) thus increasing their resilience to natural changes in the availability of suitable habitats. Modification of wetland systems and complexes disrupts connections between populations within metapopulations by increasing the distance between patches further enhancing the probability of extinction. Fragmentation of wetland habitats also leads to the decrease in the total surface area and thus in the total size of populations, as well as the size of the remaining habitat patches which increases their vulnerability.
Aquatic plants are often sensitive to changes in their freshwater environments such as increases in nutrients, changes in salinity, pH, temperature, etc. and they may be important as indicators of ecosystem health. It is therefore not surprising that pollution is a big threat and the main cause is the use of fertilisers and herbicides or pesticides in agricultural landscapes. Nutrient levels in wetlands are increasing, through run-off from agriculture, sediment leaching in from various practices which break up the soil surface, from fish-farming and from atmospheric deposition. Whilst the evidence for direct impacts of increased nutrient loads on aquatic and wetland plants is scant, they are extremely vulnerable to the knock-on effects of increased nutrient loads, developing from an increase in productivity and the replacement of oligotrophic species by meso- and eutrophic-species including aggressive colonial perennial grasses and exotic invasive species; if enrichment continues, most higher plants disappear, displaced by algal mats, phytoplankton and eventually anoxic crises. Eutrophication of large water bodies tends to slow down or decrease in developed countries; however eutrophication of headwaters is often increasing as is use of xenobiotic pollutants such as herbicides. Pollution from domestic or industrial sources and garbage disposal is affecting the ecosystem in similar ways.
Recreational use of water bodies is another threat factor; plants can suffer from excessive trampling due to recreational activities or from work activities such as removal of vegetation while "cleaning up" water bodies. Similarly, water sports have, for example, been described as a threat to Isoetes boryana which grows in shallow water on the margins of large lakes.
The invasion of exotic species such as Crassula helmsii, Ludwigia species and Sagittaria subulata leads to increased competition for space with native aquatic plants and affects most threatened aquatic plant species. Climate change and particularly an increase in droughts pose a problem for aquatic plants especially in the Mediterranean countries. The direct effect is that less suitable habitat will be available but this be aggravated by higher demand on the existing water resources in times of drought. Several consecutive dry years may also adversely affect the reproduction capacity of some species.