Mercury (Hg) remains hazardous in aquatic environments, because of its toxicity and high biomagnification in food webs. In phytoplankton and macrophytes, Hg compounds at high concentration have been reported to affect the growth, photosynthesis, and nutrient metabolism, as well as to induce oxidative stress and damage. Here, we reviewed the recent knowledge gained on cellular toxicity of inorganic and methyl Hg (IHg; MeHg) in aquatic primary producers at more relevant environmental concentrations, with a particular focus on omics data. In addition, we compared a case study conducted with transcriptomic on the green microalga Chlamydomonas reinhardtii and the macrophyte Elodea nuttallii. At lower concentrations, IHg and MeHg influenced similar gene categories, including energy metabolism, cell structure, and nutrition. In addition, genes involved in the cell motility in the microalgae, and in hormone metabolism in the macrophyte were regulated. At equivalent intracellular concentration, MeHg regulated more genes than IHg supporting a higher molecular impact of the former. At the organism level in C. reinhardtii, MeHg increased reactive oxygen species, while both IHg and MeHg increased photosynthesis efficiency, whereas in E. nuttallii MeHg induced anti-oxidant responses and IHg reduced chlorophyll content. Data showed differences, according to species and characteristics of life cycle, in responses at the gene and cellular levels, but evidenced a higher molecular impact of MeHg than IHg and different cellular toxicity pathways in aquatic primary producers.