1. Freshwater pearl mussels (Margaritifera margaritifera) in the River Dee (north-east Scotland) are in decline, and now occur at low densities with poor recruitment levels. The population's deterioration has been attributed to reduced water quality, degraded river-bed habitat and pearl fishing but the specific importance of each of these impacts has not previously been investigated.

2. This study focused on the impacts of artificial structures on the River Dee's freshwater pearl mussel population. Natural hydromorphological features were also included in the analysis. Relationships between the spatial distribution of the freshwater pearl mussel population and 31 explanatory variables were investigated using logistic regression. Three different model selection strategies were compared and contrasted.

3. An absence of freshwater pearl mussels was found to be significantly associated with the following factors: (1) presence of bank protection; (2) proximity of the nearest upstream bridge; (3) presence of a wastewater treatment works; (4) number of upstream tributaries; (5) proximity of the nearest upstream tributary; and (6) presence of sediment deposition.

4. The results strongly suggest that artificial structures on the main stem of the River Dee have contributed to the decline of its freshwater pearl mussel population. Hypotheses are proposed for the causal relationships involved. Requirements for further exploratory analyses, model testing, and experimentation are discussed.

5. This work opens a new line of investigation into the causes of the decline of freshwater pearl mussel populations, providing formal support at a catchment scale for an impact previously identified only on a site-by-site basis.