We study Nijenhuis structures on Courant algebroids in terms of the canonical Poisson bracket on their symplectic realizations. We prove that the Nijenhuis torsion of a skew-symmetric endomorphism N of a Courant algebroid is skew-symmetric if the square of N is proportional to the identity, and only in this case when the Courant algebroid is irreducible. We derive a necessary and sufficient condition for a skew-symmetric endomorphism to give rise to a deformed Courant structure. In the case of the double of a Lie bialgebroid (A,A*), given an endomorphism n of A that defines a skew-symmetric endomorphism N of the double of A, we prove that the torsion of N is the sum of the torsion of n and that of the transpose of n.