ABSTRACT: The paper outlines the current trends and challenges in studies of flow-biota interactions particularly focusing on freshwater aquatic systems. The multiple scales and a variety of mechanisms involving hydrodynamic, biomechanical and ecological processes differentiate these interactions from conventionally studied flow-structure interaction problems, and highlight the methodological and conceptual challenges to be resolved. The appearance of new promising measurement capabilities (e.g., use of high-resolution laboratory and field panoramic and stereoscopic PIV at a variety of scales), employment of advanced turbulence concepts in flow-biota considerations, accelerated advances in organism biomechanics, and developments in multiscale descriptions of multi-component systems represent the current trends that are briefly discussed and illustrated with case studies. These trends reflect the emergence of a new inter-discipline subject area - Hydrodynamics of Aquatic Ecosystems - that can be defined as a study of flow-organism interactions in running waters with particular focus on relevant transport processes and mutual physical impacts occurring at multiple scales from the sub-organism scale to the organism patch mosaic scale.