The decrease in filtrate flux of ionic azo dyes through compacted Na-montmorillonite membrane can be adequately described by (i) analytical and empirically derived transport equations, (ii) solute rejection and intrinsic retention equations and (iii) X-ray diffraction. Experiments were performed using two ionic azo dyes, Orange G (7-hydroxy-8-phenlyazo-1,3-naphthalenedisulfonic acid disodium salt), a molecular biology reagent and brilliant yellow (C.I. 24890 direct yellow 4). Filtrate samples were collected using a static head setup consisting of a longitudinal flow acrylic cylinder cell through compacted Na-montmorillonite membrane. The results indicated that there was initial rapid flux reduction for the first 3 days due to surficial fouling owing to affinity of hydrophilic organic compounds rapidly getting attached to exchange sites at the dye–membrane interface before slowing down to a quasi-steady-state (5–7 days) and gradual gelation period (8–16 days) during steady-state. The ratio of flux reduction was approximately 3:5 for brilliant yellow to Orange G. The flux values were higher than mass transfer coefficients. Flux decline for the dyes followed an exponential decay described by J ∝ 1/ t n , with n = 0.9556 for yellow dye and n = 0.8923 for Orange G. X-ray diffraction indicated that both the lower molecular weight Orange G (452.4 g mol −1) and higher molecular weight brilliant yellow (624.6 g mol −1) dyes are less preferentially retained within the basal spacing of Na-montmorillonite due to only a slight shift in the range 5.8–6° 2 θ region. The results offer a preliminary study in the fate, transport and recyclability of these ionic azo dyes through smectitic membranes.