The present study aimed to remove crystal violet (CV), malachite green (MG), Cd(II), and Pb(II) from an aqueous solution using clinoptilolite zeolite (CZ) as an adsorbent. Response surface methodology (RSM) based on central composite design (CCD) was used to analyze and optimize the process parameters, such as pH, analyte concentration, adsorbent amount, and sonication time. Quadratic models with the coefficient of determination (R2) of 0.99 (p < 0.0001) were compared statistically. The results revealed that the selected models have good precision and a good agreement between the predicted and experimental data. The maximum removal of contaminants was achieved under optimum conditions of pH = 6, sonication time of 22 min, the adsorbent amount of 0.19 g, and analyte concentration of 10 mg L−1. The reusability test of the adsorbent showed that the CZ adsorbent could be used 5 times in water and wastewater treatment processes. According to the results of interference studies, the presence of different ions, even at high concentrations, does not interfere with the removal of contaminants. Applying the CZ adsorbent on environmental water samples revealed that CZ adsorbent could remove CV, MG, Cd(II), and Pb(II) in the range of 84.54% to 99.38% and contaminants present in industrial effluents. As a result, the optimized method in this study can be widely used with high efficiency for removing CV, MG, Cd(II), and Pb(II) from water and wastewater samples.