The rationale of most restoration strategies is that with the reconstruction of natural habitats comes biodiversity, and ecosystem functioning and services will follow suit. Uncertainty and frequent failure in restoration outcomes, however, are recurrent and likely related to the complexity of ecosystem properties. Here, we propose ecological simplification as the general mechanism by which human impacts have modified cross-scale relationships among landscape complexity, integrity, and niche diversity in ecosystems. To manage and reverse the negative effects of ecological simplification, the interplay between research and management must quantify the large-scale complexity of reference to restore simplified systems and to link these measures to niche diversity quantified at finer scales. Because of their historical interaction with human societies, we use riverine floodplains as model ecosystems to review the causes and consequences of simplification and to discuss how contemporary restoration can minimize the effects of simplification on biodiversity, functioning, and services of riverine floodplains.