Mucilage-based flocculants are an alternative to synthetic flocculants and their use in sustainable water treatment relates to their non-toxic and biodegradable nature. Mucilage extracted from flaxseed (FSG) and fenugreek seed (FGG) was evaluated as natural flocculants in a coagulation–flocculation (CF) process for arsenic removal, and were compared against a commercial xanthan gum (XG). Mucilage materials were characterized by spectroscopy (FT-IR, 13C NMR), point-of-zero charge (pHpzc) and thermogravimetric analysis (TGA). Box–Behnken design (BBD) with response surface methodology (RSM) was used to determine optimal conditions for arsenic removal for the CF process for three independent variables: coagulant dosage, flocculant dosage and settling time. Two anionic systems were tested: S1, roxarsone (organic arsenate 50 mg L−1) at pH 7 and S2 inorganic arsenate (inorganic arsenate 50 mg L−1) at pH 7.5. Variable arsenic removal (RE, %) was achieved: 92.0 (S1-FSG), 92.3 (S1-FGG), 92.8 (S1-XG), 77.0 (S2-FSG), 69.6 (S2-FGG) and 70.6 (S2-XG) based on the BBD optimization. An in situ kinetic method was used to investigate arsenic removal, where the pseudo-first-order model accounts for the kinetic process. The FSG and FGG materials offer a sustainable alternative for the controlled removal of arsenic in water using a facile CF treatment process with good efficiency, as compared with a commercial xanthan gum.