The present study analyzes the weight gain patterns per unit of size and estimates the minimum suitable catch size of two clam species: the carpet shell clam Ruditapes decussatus and the Manila clam Ruditapes philippinarum. For this purpose, data from the two largest estuaries along the northern coast of Spain (Cantabrian Sea) were used. The length–weight relationship of both studied species was estimated using two models: a classic allometric model and a nonparametric regression model based on local linear kernel smoothers. Additionally, first derivatives were used to estimate a minimum capture size for this species, corresponding to the size at which the first derivative reached the maximum. Within this context, the models application showed (a) the nonparametric model resulted in a better fit of data for both species (b) different minimum catch sizes for each species based on maximum length (49.5 mm for R. decussatus and 44.7 mm for R. philippinarum), both considerably larger than the currently established in EU and (c) an effect of estuaries and zones on individuals weight gain patterns. This confirmed the nonparametric model as an alternative approach to analyze the length–weight relationship for the studied species and to estimate a minimum suitable catch size of capture. The application of the specific catch sizes obtained in this study could lead to an increase in available commercial stocks of both species and positive effects on the conservation of the native species. In addition, the estimated zone-specific weight-gain patterns and minimum catch sizes could support a zone-based management. Therefore, this study provides a preliminary study and a starting point to consider the revision of the minimum legal size of the studied species in order to improve the current shellfishery management model.