The present paper describes a new restricted access material-ion imprinted polymer for on-line preconcentration of Cd2+ from natural water samples, and simultaneous clean-up of humic acid. Cadmium-imprinted poly(allylthiourea) was synthesized and modified with 2-hydroxyethyl methacrylate (IIP-HEMA) to obtain the restricted access ability. The on-line flow injection system coupled to FAAS (FIA-FAAS) was based on percolation of 20.0 mL of the sample (pH 8.70 and in presence of organic matter) through a mini-column (100.0 mg of IIP-HEMA) at 7.5 mL min−1 flow rate. The elution step was performed using 2.0 mol L−1 HNO3 at 5.0 mL min−1 flow rate. The method provided linearity in the range 0.56–50.00 μg L−1 and limit of detection of 0.17 μg L−1. The preconcentration factor was found to be 37-fold, consumption index of 0.54 mL, preconcentration efficiency of 13.10 min−1 and sample throughput of 21 h−1. The precision of the method was evaluated in terms of intra-day and inter-day repeatability and the relative standard deviation percentage (%RSD) obtained by two-level concentration (2.50 and 40.00 μg L−1) in the presence and absence of humic acid were <5.0%. Low interferences of ions commonly found in water samples as well as the humic acid were observed. The accuracy was attested by addition and recovery tests at two-level of Cd2+ (2.00 and 20.00 μg L−1, both prepared in presence of humic acid) in a real water sample, and the recovery percentages ranged from 93.8 to 108.7%. Cadmium was also analyzed in a certified reference material TORT-2 (lobster hepatopancreas). The method was applied for Cd2+ determination on water after spiking procedure with known concentration, food (linseed, 301.8 ± 15.3 μg kg−1), herbal medicine (Ginkgo biloba L., 221.2 ± 5.8 μg kg−1) and cigarette (77.9 ± 6.3 μg kg−1).