An ultrafiltration-based process for oligosaccharide and peptide fractionation from a macroalgae subcritical water hydrolysate was studied. A wide range of separation results was obtained depending on the membrane pore. 100 kDa cut-off size was enough for hydrolysate clarification with total retention of colloidal materials. Oligosaccharides present in the hydrolysate showed the highest retention with all membranes, glucans mostly, followed by galactans, and finally arabinans. Peptides obtained after subcritical water treatment were some of the lowest rejected compounds, even using a 5 kDa membrane. The increase in temperature from 20 to 50 °C and feed flow rate from 6.6 to 11.2 L/h enhanced permeate flux for 5 kDa membrane, without perturbing the membrane retention. The Hermia's models identified the cake layer resistance as the major fouling resistance in hydrolysate filtrations at 20 °C, but standard pore blockage was the principal fouling mechanism at 50 °C. A fractionation process with sequential filtration stages at 20 °C and TMP = 1.1 bar was examined. Oligosaccharides were fractionated in the retentates of the sequential filtrations with 100, 5 and 1 kDa membranes. The final permeate collected from the 1 kDa membrane was freeze-dried to obtain a peptide-rich solid (71 wt%) that could be used in different applications.