The present study investigated the use of local and affordable clinoptilolite for the removal of persistent dyes from water. To improve its adsorption capacity, Na-clinoptilolite was modified chemically with two N-terminated siloxanes (molar mass: 2600 and 11000 g/mol) and used to adsorb the dye phenol red. The results of Fourier-transform infrared spectroscopy (FTIR) showed that N-terminated siloxanes were grafted successfully onto clinoptilolite. Examination by X-ray diffraction and scanning electron microscopy supported the suggestion of modifications observed by FTIR. The modified clinoptilolite showed improved adsorption properties for phenol red: up to 0.32 mg of phenol red were removed per g of clinoptilolite modified with N-terminated siloxanes from water, while HCl-treated clinoptilolite removed only 0.15 mg after 4 h. Langmuir and Freundlich models were used to obtain isotherm parameters. Results (with R2 > 0.84) from pseudo-first and pseudo-second order equations suggested that adsorption could have involved chemisorption and physisorption, probably because of the mineral-organic nature of the materials prepared.