This study explores diatom community dynamics in a highly modified semi-arid temperate region river system characterised by inconsistent river flow. Various water and sediment environmental variables were assessed using a multi-faceted analysis approach to determine the spatio-temporal drivers of benthic diatom communities in the river system. Overall, the diatom community was generally dominated by pollution tolerant species, reflecting the anthropogenic intensity and activities on the river system. Diatom community composition was found to be largely determined by water column chemistry variables particularly nutrient concentrations in comparison to sediment chemistry and physical variables. Strong seasonal diatom species composition was also observed and this was driven by strong seasonal variations in nutrient loads and metal concentrations, a result of the variable water flow across the two seasons. However, the greater temporal variation in communities was observed in the smaller systems with the mainstream river system being more homogenous over time. In addition, diatom community composition and environmental variables were found to be different and more pronounced between streams and mainstream sites, than between canals and streams. The study highlights the complex interaction between water column, sediment and physical variables in determining the diatom species composition in small river systems. It also highlights the importance of river flow inconsistency as an indirect variable that alters primary drivers such as nutrient concentrations in the water column and heavy metal levels in the sediment.