Western Australia contains three ichthyological provinces, each with relatively high proportions of endemic fishes and widely different climatics.  We discuss long-term studies that examine the life-cycles of fishes, their habitat use and environmental variables to determine how they could be impacted by ongoing flow and/or groundwater declines.    South-western Australia is an unfortunate global ‘pinup’ of rainfall and flow reductions due to climate change; dramatic reductions in river flow has occurred since the 1970’s; with universal agreement that this drying trend will continue.   The south of the State is seeing considerable range reductions and localised population declines of fishes.  Hydrological change is likely to continue to both directly and indirectly impact freshwater fishes of the region; many of which are threatened. We demonstrate that the strength of spawning migrations of potamodromous fishes will decline with ongoing flow reductions.  Variation in the wet season in the Kimberley region has considerable implications for fishes.  A prime example relates to the level of recruitment of a threatened catadromous elasmobranch, with pressures to extract water from the region’s large rivers potentially exacerbating a reduction in recruitment. The thirst for water resources is expanding in the Pilbara; an area where surface water is scarce and where groundwater is a potential resource of potable and industrial water.  Implications of groundwater extraction for the desert fishes which rely on it for survival are highlighted. The hydro-ecological relationships we discuss illustrate the vulnerability of freshwater fishes throughout Western Australia to altered flow regimes which are crucial to consider in water resource development.