When microalgae are exposed to contaminants, the role of associated bacteria within the phycosphere, the microenvironment surrounding algal cells, remains largely unknown. The present study investigated the importance of algae-associated bacteria on the responses of microalgae growth to metallic and organic toxicant exposure. The effects of a polluted sediment elutriate, and of metal or pesticide mixtures at environmentally relevant concentrations (<10 μg L−1) were assessed on the growth of two microalgae strains: Isochrysis galbana, a prymnesiophyte, and Thalassiosira delicatula, a centric diatom. Both cultures were maintained as axenic or bacterized under similar conditions in batch cultures. In axenic conditions, the metal mixture addition at low concentrations alleviated limitation of growth by metals for T. delicatula relative to control, but inhibited I. galbana growth at highest concentration. In similar axenic conditions, both T. delicatula and I. galbana growth were negatively inhibited by pesticide mixture at concentrations as low as 10 ng L−1. The bacterial diversities associated with the two microalgae strains were significantly different (Bray–Curtis dissimilarity greater than 0.9) but their impact on microalgae growth was similar. The presence of bacteria reduced algal growth rate by ca. 50% compared to axenic cultures, whereas no significant effect of sediment elutriate, metal or pesticide mixtures was noticed on non-axenic algal growth rates. These results show that bacteria may have a negative effect on algal growth but can reduce pesticide toxicity or metal availability to algae.