This study aims to evaluate the effectiveness of currently available substrate data to designate marine reserves to meet conservation objectives. The case study site is Lyme Bay (approx. 2460km2), in the western English Channel. An area of 240km2 in Lyme Bay was designated ‘closed to bottom dredging’ in July 2008 with the aim of protecting reefs which are an important habitat for Eunicella verrucosa (pink sea fan). The effects of using different substrate data resolution on the selection of sites to protect a range of biotopes using the Marxan package are determined. The effect of including a closed area on the efficiency of a marine reserve network is also investigated. Findings suggest that substrate data did not capture the biodiversity of the area and that using no data at all was equally effective. If low resolution data are all that are available then other options, such as expert opinion, or other data, such as activity use information could be used instead. Including a predefined closed area into the analysis led to an increase in area required to meet conservation goals using high resolution biotope data. It also increased the area of the reserve using the three substrate layers with no increase in protection for biotopes. This suggests that when designing networks of marine protected area sites, including current protected areas may be inefficient, resulting in larger areas being protected with no increased conservation of marine biodiversity. Policy makers must be prepared to adapt management in light of these findings and be aware of the shortcomings of the data available for use in marine conservation planning.