Praseodymium (Pr)-doped CdSe nanoparticles with different Pr contents were successfully synthesized by an easy hydrothermal method. The prepared samples were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM). XRD analysis demonstrated that the particles were excellently crystallized and correspond to cubic CdSe phase. SEM images indicated that the sizes of the particles were in the range of 50–100 nm. Photocatalytic efficiency of pure and Pr-doped CdSe samples was evaluated by monitoring the decolorization of malachite green (MG) in aqueous solution under visible light irradiation. Color removal efficiencies of 47.16% for CdSe and 94.32% for Pr0.06Cd0.94Se were achieved at 120 min. It was found that the presence of Cl–, SO4–2, and HCO3– ions obstructed the photocatalytic degradation of MG, but the presence of S2O82– accelerated it. Also, the effect of operational parameters at optimum conditions was modeled regarding the nonlinear regression analysis.