Freshwater mussels require stable cobble and gravel substrates. Adult mussels are two-thirds buried and juveniles, up to five years old, are totally buried within the substrate at >5 cm. They require water that is high quality, clean, oligotrophic, fast-flowing, well oxygenated and without unnatural levels of silt, algae or plant life e.g. macrophytes. In addition, the presence of sufficient salmonid fish to carry the larval (glochidial) stage of the mussel life cycle is essential.

The gravels for Atlantic salmon must be of a suitable coarseness to facilitate redd (nest) construction. Eggs will be buried 15 to 25 cm below the gravel surface, and similar to mussels, the gravels must be largely or completely free of silt and nutrient enrichment.

Of greatest concern for both species, is the low level of dissolved oxygen concentrations within the interstices (spaces between riverbed sediments) of the riverbed sediments where the juveniles live. Excess silt entering the watercourse can cover the riverbed and smother juvenile mussel and salmonids. Silt can also provide a suitable substrate for macrophytes and algae to become established. Nutrient enrichment (e.g. phosphate from run-off) also increases the potential for algal growth.

Excessive algal growth on the riverbed will prevent water and oxygen exchange to the interstices. In addition, oxygen in the river is depleted as the algae decomposes. The decomposed algal material known as flocculating organic fine material (floc) can smother the riverbed and consequently juvenile habitat.

It has been determined that flow regulation can have negative effects on mussels and fish habitat. Prolonged low flows can cause stress due to temperature increase, oxygen depletion, concentrated pollutants and reduction of silt transport. Studies into flow are currently being undertaken as part of the Compensatory Measures Project.

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