Diatom communities were analyzed in 39 streams located in drainages with varied land-use practices throughout Victoria, Australia. Thirteen water quality parameters were also measured in each stream. Most streams had low HCO3 1− concentrations (low buffering capacity) with >90% of the waters dominated by Na1+ and Cl1−. Phosphate concentrations ranged from 0.003 to 2.0 mg/L. Diatom communities (245 taxa) were strongly correlated with land-use practices, i.e. historic clear cutting, and secondary salinization. Streams influenced by heavy irrigation practices and dryland farming had reduced species diversity and richness compared to systems with low to moderate land use. A nonmetric multidimensional ordination of diatom communities in the 39 streams was conducted. An ANOSIM on the ordination showed that diatom communities in upland watersheds with native forest canopies and low salinization, lowland streams in watersheds with cleared forest canopies, moderate agricultural utilization and salinization, and lowland streams in areas with high irrigation and salinization were all significantly different (p<0.001) from one another. Community ordination techniques showed that both specific conductance (salinity) and phosphorus interacted to determine stream diatom community structure in drainages with high secondary salinization. Drainages with low to moderate agricultural activity and low nutrients, but with a wide range of salinities showed strong associations with the diatom taxa Amphora coffeaeformis, Cymbella pusilla and Entomoneis paludosa, whereas, streams in regions with heavy agricultural practices and high phosphorus had Bacillaria paradoxa, Nitzschia hungarica, N. frustulum and Aulacoseira granulata as numerically important diatoms. In contrast, Rhizosolenia eriensis, Frustulia rhomboides, Eunotia pectinatus and Tabellaria flocculosa were strongly associated with upland streams with fast current, relatively low O-PO4 3− concentrations, low pH, low salinity, and low temperature. In general, the diatom communities in saline streams (≥3 mS) were similar to those previously reported in saline lakes in Victoria.