Dams and weirs are widely implicated in large-scale declines in both the range and abundance of aquatic fauna. Although many factors are involved, such declines are commonly attributed to the prevention or reduction of migration, reductions in available habitat, alteration of natural flow regimes and changes to physicochemical characteristics. In Australia, studies into the ecological effects of these impacts are limited, and have concentrated mainly on species of recreational and commercial importance. Subsequently, the adverse effects of dams and weirs, and suitable methods of mitigation, remain largely unknown for many other taxa. Therefore, the major aim of this thesis is to investigate the ecological effects of dam and weir construction on previously unstudied migratory assemblages of fish and macroinvertebrates in the Murray-Darling Basin. It is anticipated that the results of these studies will feed back into improved management strategies that help arrest the previously observed declines of aquatic fauna. Initially, fish communities were sampled, by boat electrofishing, from both reference sites and downstream of Balranald and Redbank weirs on the lower reaches of the Murrumbidgee River, Australia. Sampling was stratified over large spatial and temporal scales to gain a comprehensive understanding of species most affected by the presence of these two barriers. In general, the weirs obstructed fish migrations during summer and autumn and many species of small-bodied fish such as Australian smelt, western carp gudgeon, fly-specked hardyhead and crimson-spotted rainbowfish accumulated downstream of Balranald Weir. In addition, downstream accumulations of juveniles of larger-bodied species such as bony herring, common carp and goldfish were also detected. Although many previous studies had either documented or hypothesised that upstream migrating fish accumulate downstream of migration barriers, none attempted to quantify the size of such populations. Therefore, a simple but efficient method to estimate the size of migratory populations was assessed at the Balranald Weir site. The application of two commonly used estimation techniques yielded relatively reliable results for seven species that accumulated downstream of the weir. Population size estimates were greatest for most species during summer and autumn, where accumulations as high as 800 fish per day were detected. The largest calculated population size estimates, in addition to the greatest temporal variation, of any individual species was observed in bony herring. Given the simplicity of the technique and the relative accuracy of population estimates, it was concluded that these methods could easily be applied to other weirs where the size of migratory populations is of particular interest. A study investigating the effects of Yanco Weir on the diets of three migratory percichthyid species, Murray cod, trout cod and golden perch was also conducted. Observed spatial variation in a number of trophic processes strongly implicated Yanco Weir as a major contributor to increased competition among percichthyid species on the Murrumbidgee River. The greater relative abundance of percichthyids from downstream samples, combined with increases in dietary overlap and a greater percentage of empty stomachs, also suggested percichthyids may be significantly affecting the relative abundance of potential prey items such as freshwater prawns and Australian smelt. These significant changes in dietary composition were likely related to migratory behaviour, as these species accumulated downstream of the weir, and could be readily expected at other sites where passage is obstructed. It was suggested that the construction of suitable fish passage facilities would effectively reduce the probability of migratory fish accumulating and, subsequently, potential effects of dams and weirs on trophic processes. Since it was established that dams and weirs of the Murrumbidgee River were significantly affecting migratory fish communities, an innovative but relatively inexpensive fishway design, the Deelder fish lock (after Deelder, 1958), was constructed and assessed for wider application throughout the Murray-Darling Basin. The Deelder lock was effective at mitigating the effects of Balranald Weir by providing passage for a wide range of size classes and species of fish; but importantly, the structure enabled the passage of most species previously observed to accumulate downstream of the structure. Most significant was the ability of the fish lock to pass substantial numbers of small-bodied fish, which were previously not considered migratory, suggesting that these species should be considered when developing options to mitigate the effects of other dams and weirs throughout the Murray-Darling Basin. A significant finding of this study was the realisation that substantially more species and size classes of Australian native fish are migratory than previously thought. Subsequently, it is recommended that, when designing facilities to mitigate the effects of a dam or weir, the structure of the entire migratory community is considered when developing operating parameters. Various options for mitigating the effects of dams and weirs are discussed, but it was concluded that the construction of effective fishways would be the most appropriate means of restoring migration pathways to Australian native fish. A strategic approach for assessing and adaptively mitigating the effects of dams and weirs is presented and discussed.