The Ramsar-listed Coorong lagoon lies at the terminus of the Murray-Darling River system in South Australia. Diatom and foraminifera relationships with water quality were characterised in order to develop diatom- and foraminifera-based models with the potential to infer water column salinity. Seventy-four samples were collected during 2007, a year of continuing drought in the catchment, and of no discharges at the Murray Mouth. The sample sites had a salinity gradient of 1.8–190 g l−1 total dissolved solids. The diatom data set comprised 215 taxa, while there were only eight taxa in the foraminiferal data set. Canonical correspondence analysis of diatom species-environment relationships showed that salinity explained the largest proportion of diatom variance. Hence, a diatom-based salinity transfer function with reasonable predictive power (measured vs. diatom-inferred salinity r jack 2 = 0.82; Root Mean Squared Error of Prediction = 16 g l−1) was developed. Application of the transfer function to fossil diatom assemblages from The Coorong suggested that pre-European salinity values were generally >50 g l−1 and that salinity declined following settlement. These results, however, contradict the recent history of The Coorong where there have been substantial lagoon-wide salinity increases. The pre-impact diatom flora has no analogue in the modern data set, highlighting the degree of departure from past conditions. CCA of the foraminiferal data set identified salinity and total nitrogen as the variables with the greatest explanatory power. However, accurate predictive models could not be developed using either variable due to low foraminiferal abundance and species richness. These factors may have been a consequence of diminished foraminiferal recruitment rates over successive years, an artefact of reduced marine water input to The Coorong. Future attempts to generate predictive models from this region would benefit from the inclusion of data from distant locations, since suitable analogue sites do not exist in close proximity. The study has generated useful insights to the apparently broad salinity tolerances for several cosmopolitan diatom and foraminifera species, and has identified a number of diatom and foraminifera taxa that may prove useful in the qualitative interpretation of down-core trends in The Coorong and the lower Murray River region.