Increasing salt concentration in tributaries from catchments and rising water tables are the prime contributor to environmental degradation of rivers, creeks, streams or other water bodies. This is especially true during periods of mid- and low stream flows in arid and semi-arid regions around the globe. Catchment scale studies suggest that management of stream salinity requires greater land use change than is economically viable. Therefore, rather than focusing on the opportunity cost of catchment scale interventions, exploring interventions that are potentially viable at farm scale could be an appropriate strategy for stream salinity management. This paper presents an analysis of alternative on-farm strategies, such as evaporation ponds and serial biological concentration of salts, aimed at developing an economically self-sustainable stream salinity management system for the Box Creek stormwater escape channel located in the Murray–Darling Basin (MDB), Australia. It is concluded that irrigation areas, with careful management of flows in tributary streams, may be able to play a role in safeguarding the Murray River against further salinisation from irrigation and dryland areas. The outcomes of this paper will be helpful, but not limited to, the MDB in addressing environmental, economic and social issues associated with management of salt concentration in tributaries.