We used Tasmania to demonstrate how outputs from downscaled climate models could be integrated with spatially resolved hydrological models and freshwater biodiversity data. In consultation with stakeholders, we quantified how different climate change scenarios could affect the risks to biodiversity assets, documented the scope and types of adaptation actions, and assessed the strengths and weaknesses of the policy and planning instruments in responding to climate change. We concluded that downscaled climate predictions linked with modelling of catchment and hydrological processes now refine projections for climate-driven risks to aquatic environments. Spatial and temporal hazards and risks can now be compared at a variety of scales via Bayesian Belief Networks, as well as comparisons between biodiversity assets. Uncertainties can be identified and built into adaptation processes. Notwithstanding this progress, we identified the following obstacles to implementation.Biodiversity data sets need to be improved and updated, and better, spatially explicit information on the contributions of groundwater to surface waters is needed. The bewildering array of adaptation tools available to stakeholders needs to be organised using procedures such as scenario modelling which incorporate explicit tools for comparing costs, benefits, feasibility and social acceptability so that priorities can be set transparently. Formal mechanisms for the uptake of knowledge about identified risks into policy and legislative instruments remain undeveloped. The greatest challenge is to integrate multiple adaptation strategies (sometimes at different scales) to achieve specific adaptation objectives—especially where a mix of water management and non-water management is required.