The waters of the whole SAC are relatively turbid which limits the water depth to which seaweeds within the SAC can survive. Sediment type has a strong influence over the types of marine species which are associated with intertidal and subtidal sediment areas within the SAC. The surface of the sediment is often apparently devoid of vegetation, although mats and films of micro-algae are common.

Muddy areas are highly productive, containing high levels of organic material and are very important to the marine ecosystem, playing an important role in marine food chains. They generally support very large numbers of an individual few species. Diversity of various species, including marine worms tends to increase with increasing levels of sand and gravels, particularly where conditions result in sediments being muddier. In areas of coarse sand, where the sediment is of similar grain size, the sediment is easily moved by waves and tides and only a few specialist species are able to exist in these areas.

Strong tidal streams result in characteristic communities, dominated by filter feeding animals fixed onto or into the seabed, typically including soft corals, hydroids (sea firs), bryozoans (sea mats), large sponges, sea anemones and mussels. The fast-flowing water brings a good supply of food and nutrients, supporting the growth of these animals and, in many areas of the strait, sponges are able to grow to unusually large sizes.

In areas of extremely strong tidal currents, species are restricted to those that grow as thin encrusting layers across the seabed, anything larger would get swept away. The lack of strong wave-action within much of the SAC results in the rocky shores being dominated by seaweeds like the serrated wrack Fucus serratus and kelps such as oarweed Laminaria digitata. Areas within the SAC which are exposed to moderate wave-action, such as the north Penmon coast are dominated by a mixture of seaweed, mussels and barnacles, which are resistant to dislodgement by waves.

Waves can also influence the size and shape of animals and plants. For example, mussels found on rock habitats in sheltered areas within the strait are much larger than those on the north Penmon coast because they are able to open their shells and feed more frequently in the more sheltered conditions.

The nationally scarce dwarf eelgrass Zostera noltii is found in the area between Beaumaris and Lleiniog.