The seasonal variation and spat recruitment pattern of the scallops Flexopecten glaber and Chlamys varia in the protected aquatic ecosystem of the northwestern Amvrakikos Gulf (Natura, 2000) were examined by using a combination of plankton sampling and spat collection techniques during the spring and summer of 2007. The presence of the larvae was reported in all samples from the beginning of May to the end of August. Peak numbers were obtained at the beginning of June and in mid-July. The highest settlement density was recorded at a depth of 8 m below the surface, indicating the most suitable placement for the spat collectors despite the hypoxic bottom layer underneath.