Presence-only data based habitat suitability (HS) modelling is proposed as an adequate tool to determine environmentally homogenous zones that support sampling strategies and face limitations associated to spatial interpolations in shellfish stock assessments. For the first purpose, together with geostatistic tools, HS modelling would be applied to classified different habitats. A statistically representative number of sampling stations would be located within each habitat class. In these environmentally homogeneous areas, the biomass of the studied shellfish populations would be estimated. For the second purpose, the HS-based methodology to estimate standing stocks is described. A regression curve linking biomass and habitat suitability is calculated using previously obtained biomass-HSI paired values. The obtained regression model is, in turns, integrated in the raster-based habitat suitability map, using ArcGis, to estimate the biomass spatial distribution. The method would also contemplate biomass predictions from the initial calculations through the incorporation of capture and recruitment data.