Conserving harvested animal populations needs to adequately account for species-environmental variability in life history traits to ensure that harvest rules result in consistent population effects across a species distribution. To better understand the effects of temperature and harvest in a threatened freshwater crayfish (the Murray Crayfish Euastacus armatus), we employed linear and generalised linear mixed models to explore relationships between water temperature and crayfish size, and reproductive state (size at functional reproduction- SFR; females with eggs), across three lowland and two upland populations in south-eastern Australia. An age-, size- and sex-structured stochastic population model for E. armatus, incorporating field data, was used to assess population level impacts (Expected Minimum Population Size, EMPS) through a comparison of estimated total reproductive capacity (TRC) values among study populations. Crayfish size, and SFR were correlated with water temperature; crayfish populations in cooler upland waters were smaller and reproduced at a smaller size (decreased SFR) than crayfish from warmer lowland rivers. The exception to this trend, was the lowland Goulburn River crayfish population, whose size structure and SFR was more closely aligned with upland populations, likely due to depressed water temperatures due to a low-level dam outlet. Smaller size at functional reproduction and therefore lower SFR of upland populations significantly reduced the risk of these populations declining from harvest, compared with lowland populations. This provides support for current ‘harvest slot legal length’ rules protecting upland populations; however, this places lowland populations at increased risk from harvest. Our improved understanding of the relationships between temperature, size, SFR, harvest and total reproductive capacity highlight the value of considering plasticity in life history traits for supporting the conservation of threatened freshwater .