Reversing the effects of secondary salinization, and its impacts on aquatic biodiversity, is a growing global challenge, and particularly prevalent in Mediterranean-climate regions. Remnant freshwater tributaries in salinized landscapes provide significant biodiversity values, including discrete areas of refuge, dilution of salinized reaches, and potential source populations for recolonisation. The importance of these areas for aquatic fauna is widely accepted but rarely evaluated in the field. This study explored how spatial distribution of southwestern Australia's only freshwater mussel species, Westralunio carteri, has responded to the ongoing salinity trend in the Kent River catchment. Our results showed that salinity in the river has begun to reverse following improved catchment management, and also detected the first evidence of an associated recovery of the freshwater mussel population. Mussels in the mainstem were limited to sites around and downstream of a permanently flowing freshwater tributary, suggesting that dilution from this source provides a refuge in the lower reach. At two of those sites, all individuals were <15 years of age, indicative of recolonisation coinciding with salinity reversal around the turn of the century. Interestingly, mussels clearly persisted in other parts of the lower reach throughout the peak salinity period, when salinities regularly exceeded laboratory derived toxicity thresholds for the species. Mussels were not found in the majority of the mainstem or in highly acidic parts of the freshwater tributaries. The presence of old shells at those sites shows that the species was once widespread, and that the current distribution probably reflects a contraction due to historical salinization as well as acidification. Overall, our results show that the W. carteri population in the catchment has taken a first step towards recovery, and highlights the importance of freshwater tributaries in providing both refuge from disturbance and a source of new recruits.