The influence of lignin content on nanocellulosic fibril morphology, charge, colloidal stability and immobilization has been systematically investigated employing a series of nanofibrillated cellulose (NFC) with varying residual lignin content and compared to those of NFC made from fully bleached pulp. The lignin-containing pulps were obtained from the fractionation of Eucalyptus globulus wood chips in gamma-valerolactone (GVL)/water under the same conditions, they differ by the intensity of washing for lignin removal. The reference pulp originated from another cook of eucalyptus wood chips, and was fully bleached with a short Elemental-Chlorine-Free (ECF) sequence. All the pulps have a comparable hemicellulose-to-cellulose ratio and CED viscosity. NFC suspensions of 1 wt% concentration were mechanically produced from fluidization. The results indicated that the fibrils morphology, thickness and corresponding flocculation within NFC suspensions was highly influenced by the presence of lignin unevenly distributed on the fibril surface and within the suspension as particles. The presence of lignin in NFC suspension had a large impact on the rheology and dewatering of the NFC. Samples with high lignin content had distinguishable viscoelastic properties due to the greater flocculation of thicker fibrils and lower gel-like characteristics, with better dewatering properties.