The objective of this paper is to discuss current status and issues on inland fisheries carried out in middle reaches of Hii River, San-in area, Japan where the total fish catch of Plecoglossus altivelis has significantly been decreasing. There exist three main issues to be resolved for achieving sustainable inland fisheries in middle reaches of Hii River; transverse hydraulic structures that would prevent aquatic species from migrating toward upstream, hydrologically-driven regime shifts of the status of rock-attached algae: a staple food of P. altivelis, and excessive predation pressure from Phalacrocorax carbo. This paper reviews the three issues, and presents current challenges and future perspectives for their resolution from the viewpoint of modern mathematical modelling.