We introduce Lie-Nijenhuis bialgebroids as Lie bialgebroids endowed with an additional derivation-like object. They give a complete infinitesimal description of Poisson-Nijenhuis groupoids, and key examples include Poisson-Nijenhuis manifolds, holomorphic Lie bialgebroids and flat Lie bialgebra bundles. To achieve our goal we develop a theory of generalized derivations and their duality, extending the well-established theory of derivations on vector bundles.