To synthesize chitosan nanoparticles (CS NPs), ionic gelation is a very attractive method. It relies on the spontaneous supramolecular assembly of cationic CS with anionic compounds, which leads to nanohydrogels. To extend ionic gelation to functionalized CS, the assessment of CS degree of substitution (DSCS) is a key step. In this paper, we have developed a hyphenated strategy for functionalized CS characterization, based upon 1H, DOSY and, when relevant, 1D diffusion-filtered 19F NMR spectroscopies. For that, we have synthesized two series of water-soluble CS via amidation of CS amino groups with mPEG2000-COOH or fluorinated synthons (TFB-COOH). The aforementioned NMR techniques helped to discriminate between ungrafted and grafted synthons and finally to determine DSCS. According to DSCS values, the selection of CS-mPEG2000 or CS-TFB copolymers can be made to obtain, in the presence of hyaluronic acid (HA) and tripolyphosphate (TPP), CS-mPEG2000-TPP/HA or CS-TFB-TPP/HA nanohydrogels suitable for drug delivery.