In this paper, we explore the applicability of the Sinc- Collocation method to a three-dimensional (3D) oceanography model. The model describes a wind-driven current with depth-dependent eddy viscosity in the complex-velocity system. In general, the Sinc-based methods excel over other traditional numerical methods due to their exponentially decaying errors, rapid convergence and handling problems in the presence of singularities in end-points. Together with these advantages, the Sinc-Collocation approach that we utilize exploits first derivative interpolation, whose integration is much less sensitive to numerical errors. We bring up several model problems to prove the accuracy, stability, and computational efficiency of the method. The approximate solutions determined by the Sinc-Collocation technique are compared to exact solutions and those obtained by the Sinc-Galerkin approach in earlier studies. Our findings indicate that the Sinc-Collocation method outperforms other Sinc-based methods in past studies.