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Ion transport, often described by the Poisson--Nernst--Planck (PNP) equations, is ubiquitous in electrochemical devices and many biological processes of significance. In this work, we develop conservative, positivity-preserving, energy dissipating, and implicit finite difference schemes for solving the multi-dimensional PNP equations with multiple ionic species. A central-differencing discretization based on harmonic-mean approximations is employed for the Nernst--Planck (NP) equations. The backward Euler discretization in time is employed to derive a fully implicit nonlinear system, which is efficiently solved by a newly proposed Newton's method. The improved computational efficiency of the Newton's method originates from the usage of the electrostatic potential as the iteration variable, rather than the unknowns of the nonlinear system that involves both the potential and concentration of multiple ionic species. Numerical analysis proves that the numerical schemes respect three desired analytical properties (conservation, positivity preserving, and energy dissipation) fully discretely. Based on advantages brought by the harmonic-mean approximations, we are able to establish estimate on the upper bound of condition numbers of coefficient matrices in linear systems that are solved iteratively. The solvability and stability of the linearized problem in the Newton's method are rigorously established as well. Numerical tests are performed to confirm the anticipated numerical accuracy, computational efficiency, and structure-preserving properties of the developed schemes. Adaptive time stepping is implemented for further efficiency improvement. Finally, the proposed numerical approaches are applied to characterize ion transport subject to a sinusoidal applied potential.