There are several factors affecting scallops during the metamorphosis process that could explain the relatively low post-larvae yield observed in hatcheries. Competent bivalve larvae respond to different settlement cues to undergo metamorphosis and without adequate cues, larvae delay their metamorphosis. The objective of this study is to improve the settlement ratio of the two scallop species, Placopecten magellanicus and Pecten maximus by physical cues associated with hydrodynamic conditions, stocking density in settlement units and larval size at time of transfer to settling units. For each treatment, physiological condition was determined by fatty acid analysis to determine the energetic reserves and structural lipids. We observed similar results for the two important commercial pectinid species and validate the hypothesis on the positive effect of increased flow rate and larval size after transfer to settlement systems on settlement success. Increasing flow rate also affects positively the physiological condition of settled post-larvae by a higher accumulation of total fatty acids in neutral lipid fractions. Furthermore, no effect of larval stocking density until 90 larvae cm−2 in the downwelling sieves was observed. To our knowledge this study is the first to characterize the effect of seawater flow rate on settlement success of different pectinid species cultured under similar conditions. The experiments were performed in a close to commercial scale and thus are relevant to industry situations.