A fixed link might result in a small blocking of the water flow to the Baltic and have (local) effects on the mixing of water in the Fehmarnbelt due to the bridge piers or the possible ventilation island(s) for an immersed tunnel solution. Any effects on the water flow are so small that they can’t be measured and must be calculated with computer models. These hydrographic effects are some of the most important effects to be investigated in detail as part of the coming environmental investigation programme.

Even though most of the Fehmarnbelt is not designated as a Special Protected Area under the EU Wild Birds Directive by the authorities, the Fehmarnbelt represents an important bird area with migration routes of terrestrial birds (southwest-northeast) and crossing migration routes of seabirds (west-east). The most important breeding, staging and wintering areas are located far away from the planned construction zone. According to the results of the preliminary investigations the risk of birds colliding with the bridge structures can be considered quite low and will not endanger the bird populations as such. Future investigations will address the species, quantity and sensitivity of migratory birds in the Fehmarnbelt area in more detail and will assess the possible impacts.

During the construction phase environmental impacts on flora and fauna in the sea and on the seabed will appear in the nearfield of the construction area due to noise and spreading of spilled seabed materials from dredging and reclamation activities. These impacts will, though, predominantly be of a temporary nature (3–4 years) and will be limited to smaller areas in the vicinity of the possible bridge piers or the tunnel trench. Through careful planning and selection of best available technologies, impacts on marine flora and fauna are not expected to be detectable at a few kilometres distance away from the construction site. The bridge piers/pylons will cause a permanent loss of habitats in the sea and on the seabed.

Emissions of air pollutants like, e.g., CO2 will be reduced  due the fixed link, provided the high energy consuming ferry service ceases its operations. This reduction will be noticeable both in the short and longer term and even despite the expected increase in car traffic across the Fehmarnbelt due to the establishment of the fixed link.