The hydraulic characteristics of lotic systems are fundamental to ecological processes and patterns. In the lower River Murray, Australia, upstream dams and diversions have altered hydrology, whilst sequential low-level weirs have fragmented and homogenised a once lotic system. In this paper we (1) use modelling and empirical data to quantify changes to riverine hydraulics (i.e. river level and water velocities) since regulation, (2) propose that these changes have impacted riverine biota and processes, and (3) present modelled data and discussion on the efficacy of weir lowering and removal to conserve/restore lotic habitats, processes and biota. The weirs have raised river level and reduced river gradient and discharge–water velocity relationships, which when coupled with altered hydrology has resulted in overall declines in water velocities. Under regulated low flows (i.e. <10,000 ML day−1), which predominate, permanent lotic habitats (i.e. mean cross-sectional velocities >0.3 m s−1) now exist only in the upper reaches of a few weir-pools and anabranches, and are not restored to large reaches of the river until discharge is ≥20,000 ML day−1. We demonstrate that lowering/removing weirs has the capacity to enhance the area of lotic habitats at discharges <30,000 ML day−1. Whilst weir lowering/removal has socio-economic implications (e.g. lowering water supply offtakes), we provide the ecological rationale behind such actions and seek to promote discussion of their applicability for restoring a lotic ecosystem.