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Diatoms are siliceous micro-algae and have been used with increasing frequency as bioindicators in aquatic ecosystems. Typically, European diatom indices have been modified and augmented with data on taxa endemic to and commonly found in other parts of the world. In order to further test the application of diatom indices, water quality and diatom sampling were performed in the Bloukrans River system, Eastern Cape Province of South Africa. Nine sites with contrasting water quality were sampled along the length of the river in February, May and July 2018. Multivariate statistical analysis (Canonical Correspondence Analysis) was employed to elucidate spatiotemporal differences in diatom community structure. Canonical correspondence analysis indicated that differences in diatom community assemblages were best explained by dissolved oxygen, temperature, nitrate, conductivity and phosphate. Diatom-based indices incorporated in OMNIDIA software were also applied to assess the integrity of the water quality as indicated by diatom communities. Several foreign indices (e.g. the trophic diatom index (TDI), biological diatom index (BDI)) and the South African Diatom Index (SADI) were used in the study. The SADI demonstrated that the Bloukrans River was impacted and had significant correlations with water quality variables (p <.05). We therefore recommend the wider use of the SADI as an indicator of water quality conditions in South African lotic systems. • Anthropogenic perturbations in Bloukrans River system can be assessed using diatom indices and multivariate analysis. • High levels of nitrate, phosphate and conductivity were recorded in downstream urban sites. • Patterns of diatom assemblages were different between sites. • The South African Diatom Index (SADI) showed significant strong correlations with all water quality variables considered. • The South African Diatom Index (SADI) is also applicable for the Eastern Cape river systems. [ABSTRACT FROM AUTHOR]