Natural resource management decision making by Catchment Management Authorities in NSW is being aided by a project involving bio-physical modelling and the development of an alternative decision-making framework. The objective of the bio-physical modelling process is to generate predictions of environmental or natural resource outcomes rather than project outputs. These outcomes can then be used in an investment framework to help priority setting and project decision making. Questions that arise in bio-physical modelling include those relating to scale and scope. Scale issues include how to address the landscape impacts of particular (or a series of local) on-ground works proposals. Scope issues include assessment of multiple-attribute responses to particular changes. In a multi-disciplinary context the challenge is then to translate this information into units that can be adapted to a decision-support framework. Existing Catchment Management Authorities decisions are often based on scoring and weighting of environmental improvements using an environmental benefits index, however other economic frameworks are possible. We discuss the important context for these questions in the decision making framework.