Investment in natural resource management (NRM) by regional organisations in Australia has been widely criticised for failing to achieve substantial environmental outcomes. The Investment Framework for Environmental Resources (INFFER) is a tool for developing and prioritising projects to address environmental issues such as water quality and biodiversity decline, environmental pest impacts and land degradation. It aims to achieve the most valuable environmental outcomes with the available resources. During 2008 and 2009 INFFER has been implemented with a number of catchment management organisations (CMOs) throughout Australia. In this paper, we report on lessons from and implications of this experience. Data on implementation were collected in formal and informal ways from staff of organisations that were using INFFER and state agencies, including: an on-line survey, benchmarking questions at training workshops, a formal on-going monitoring and evaluation process tracking the use of INFFER by CMOs, and comments made in correspondence and informal feedback to the INFFER team. In this paper we describe issues that arise when implementing INFFER with regions and organisations, and how the INFFER team has attempted to address these. Key issues include a desire to consider the community as an asset and emphasise capacity building, a rejection of the need for targeted investment, and various difficulties associated with specific aspects of the Framework. Existing institutional arrangements, and the legacy of past institutional arrangements, remain serious barriers to the adoption of methods to improve environmental outcomes from NRM investment. A lack of rigour in investment planning has become accepted as the norm, and resistance to processes to improve rigour is common. However, many CMOs want to achieve better environmental outcomes with their limited funds, and we report on our efforts to work with them to achieve this by using INFFER.