Research into fluvial dunes spans disciplines, studies at grain to reach scales, and methodological approaches that include theoretical, experimental, numerical and field investigations. Despite significant research efforts to date, it remains difficult to provide definitive answers to some fundamental questions regarding dunes. This paper reviews three notable challenges that remain regarding fluvial dunes, namely scale-consistent linking of bed morphologies with turbulent flow fields, the intriguing question of what causes trains of highly-ordered sediment waves to form in beds of river sediments, and how to define the important characteristics of a dune-covered bed, including lengths, shapes, and their statistical nature. In each case, the particular challenge is discussed and then recent research and ways forward are presented. Copyright © 2010 John Wiley & Sons, Ltd.