Concentration polarization and transport through pores are used to explain the permeation of eosin dye through a nanofiltration membrane. Due to the ionic character of the dye, fixed charges in the membrane pores affect the permeation of the dye. Two transport coefficients, namely, hindered coefficients for diffusion and convection, steric hindrance factor of dye, and pore charge density are estimated by minimizing the error involved between the experimental and calculated permeate flux and concentration values. Contributions of electrical migration, convection, and diffusion towards the solute flux, have been quantified. It is found that more negative fixed charges on membrane pores leads to reduced dye concentration in the permeate.