Dispersions of nanofillers into aqueous and solid biopolymeric matrices were studied from the physicochemical viewpoint. This work was carried out based on the idea that the combination of biopolymers, derived from renewable resources, and nanofiller, environmentally friendly, may form a new generation of nanomaterials with excellent and unique properties at low cost. To this purpose, two pectins with different degrees of methyl esterification and nanoclays like halloysite and laponite RD were selected. The thermodynamic and structural studies on the aqueous mixtures of pectin and nanoclay were able to discriminate the interactions, which control the adsorption of pectin onto the filler and the aggregation of both pectin and clay particles. The gained insights were useful to interpret the mesoscopic structure of the nanocomposites (prepared from the aqueous mixtures by means of the casting method) evidenced by SEM, thermal stability, tensile properties, and transparency investigations. The attained knowledge represents a basic point for designing new hybrid nanostructures in both the aqueous and the solid phase for specific purposes.