Ports and harbours around the UK coast, and the estuary and bay habitats in which they lie provide shelter and safe anchorage for ships and boats. However, the anchoring of vessels may disturb or damage animals and plants on the seabed, either temporarily by increasing suspended sediments from the disturbance of the bottom or through direct contact with dragging anchors. The effects are of most concern in areas with sensitive or slow growing species, such as shellfish beds, soft corals, sea grasses and maerl. Disturbance from anchoring depends upon the frequency, magnitude and location of activity, type of sediments, and the sensitivity of benthic communities. Where the seabed sediments are soft and there are no sensitive communities or other underwater obstructions, damage caused by anchoring is likely to be minimal and any disturbance is generally temporary, although disturbance in low energy environments can be more than temporary. However, when anchoring over sensitive rocky communities the effects may be more damaging, for example on subtidal reef habitats. However, anchoring is often already restricted or discouraged in areas containing debris, wrecks and other obstructions, typical of uneven rocky bottom areas, which are referred to as foul ground on navigational charts. The impacts from mooring vessels depend on the type of mooring involved.

There have been concerns expressed that the location of moored craft close to the shore may cause disturbance through noise and vessel movements, particularly where it is adjacent to intertidal feeding areas used by birds. However, there appears to be very little literature and evidence that supports this view. The existence of tall yacht masts does not seem to constitute a line of sight obstruction for those birds that are sensitive to such a constraint. In most leisure mooring areas, the number of times a vessel is moved per year is very low and such movements are concentrated into a few hours on Saturday mornings and Sunday evenings. Disturbance levels are therefore minimal. Where drying moorings exist, the moorings can only be used when the intertidal areas are covered, thus eliminating any disturbance to feeding birds.

The existence of a permanent mooring area close to a wildlife site has the effect of keeping vessels that are likely to cause a disturbance through noise or wash, such as high speed recreational craft, water skiers and personal water craft, further away from intertidal habitats. In such circumstances mooring areas can provide a positive protection to designated features. Mooring areas also represent an area where restrictions are in place for human safety reasons, including speed limits and fishing bans. Mooring areas therefore represent a haven where impacts that may normally exist in an area are at a reduced level. In one example, civil law (an injunction) was used to prevent clam fishermen from dredging in a mooring area and damaging the mooring gear after they had extensively fished the rest of the harbour. In this case the mooring area was effectively a nursery.

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