The need for public investment to address loss of biodiversity in agricultural landscapes is well recognised, yet there is little analysis of the likely benefits of land-use change for regional biodiversity or the cost effectiveness of different investment options. We estimated benefits for biodiversity and cost effectiveness of different investment scenarios over 50 years for a farming area in south-eastern Australia. Declines in biodiversity were predicted under status quo land use. Implementing actions in the investment scenarios improved biodiversity status only slightly, compared with status quo land use. Future biodiversity status differed little between biodiversity-focused investment and salinity-focused investment. Biodiversity status equalled or exceeded current status only for investment scenarios with much more extensive revegetation than in catchment targets. Cost effectiveness of biodiversity improvement varied greatly between investment strategies. Biodiversity improvement was more cost effective when investment to meet catchment targets was focused on revegetation for salinity management rather than on high conservation value areas, because of lower opportunity costs for salinity management. With enhanced investment, the cost effectiveness of biodiversity improvement was greater when actions were in high conservation areas. Although improvements in biodiversity were small under the changed farming system scenarios, their cost effectiveness was higher than the other investment scenarios. Regional scale improvements in biodiversity in farming areas will require increased stewardship payments or other economic incentives for landholders.