Few ecotoxicity studies are available on thorium (Th) which hinders the ability to evaluate its ecotoxicological risk. Its release in the environment is often associated with the extraction of rare earth elements and uranium, as well as the field applications of phosphate fertilizers. This study investigates the effects of Th on microbial communities of periphytic biofilms. Ceramic plates were left to colonize for one month in the laboratory with a biofilm sampled from Cap Rouge river (QC, Canada). Plates were randomly placed in channels containing culture media representing three different conditions: a control condition (C0; background Th concentrations of 0.004 ± 0.002 nM), a low Th concentration condition (C1; 0.18 ± 0.09 nM Th) and a moderately high Th condition (C10; 8.7 ± 3.4 nM) for up to 4 weeks. The presence of Th modified the diatom community by changing its taxonomic structure, reducing diversity and increasing cell density. The taxonomic structure of the bacterial community, followed by 16S metabarcoding analysis, was affected with a significant decrease in Pseudanabaena and Shingopyxis genera in the two Th exposed conditions. No direct toxic effect of Th was observed on counted micromeiofauna but the changes in diatom and bacterial communities could explain the higher number of individual diatoms and micromeiofauna observed in Th-exposed conditions. This work shows that low concentrations of Th can modify biofilm structure, which, in turn, could disturb its ecologically key functions.