The sites waterside location has meant that understanding the potential impact on marine ecology has been an important consideration.
The diversity of plants and animals living in the Annat Narrows is low due to the slightly reduced salinity and the abrasion caused by moving sediment, but winkles, limpets, barnacles and mussels are present as well as species of red algae amongst the kelp. Colonial animals called hydroids are found in the areas which are too deep for algae.
The area is important for otters and a holt has been identified along the shore adjacent to the site. Harbour porpoises are also common summer visitors to Loch Linnhe and are sometimes seen in the vicinity of the Annat Narrows along with the more familiar common seals.
Although there are some small salmon and sea trout rivers flowing into Loch Linnhe, the most important movement of these migratory fish occurs as they make their way to the River Lochy. The fish swim past the mouth of the river, through the narrows and into Loch Eil before returning and passing up stream in the mouth of the Lochy by Fort William. In addition there is a mussel farm in the designated shell fish growing water in Loch Eil. There is also some small scale creeling for prawns in the deeper muddier area of Loch Eil.
The biomass energy plant would abstract sea water from the Annat Narrows and use it for cooling in the plant. The outfall and intake pipes would be constructed across the beach to the Narrows . During this process some sediment would be disturbed along the construction corridor and fine sediment released into the water column. The disturbed areas would return to normal within a year or so provided the same sediment is replaced. Fine sediment released would be carried by the current but would fall out of suspension relatively quickly. The design would not affect the otter holt during construction and the generation of underwater noise during that phase would be avoided in the summer period when porpoises may be present in the area.
Heated water, a by-product from the plant, would be returned to the Narrows with the addition of special additives designed to prevent marine animals growing in the internal pipework and clogging it up. The Scottish Environmental Protection Agency controls how this would be managed. There is no need to use or discharge chemicals which would accumulate in the environment and cause long term harm and no effects on the shell fishery or wider communities in the Narrow are predicted. The discharge wouldnot deter the passage salmon and sea trout and the intake and effluent pipes would be covered with a grill to prevent the entrapment of fish.