This paper describes an attempt to observe the changes in diatom composition and its ecological structure in the water bodies under oil pollution on the territory of the Varknevkhiyakha River Basin. It was revealed that species richness and especially diatom assemblages structure are the main indicative characteristics. The portion of indicative diatom groups (alkaliphilic, α-, α-β-, β-mesosaprobic) reaches its maximal level under pollution. Total abundance, species richness and diversity indexes of diatoms are smaller in this case. Ecological structure of diatom assemblages and species diversity change. They can be used for ecosystem conditions assessment.