The biogeochemical cycling of mercury in aquatic ecosystems is a multifaceted process influenced by various factors, including ambient temperature, seasonal fluctuations, the activity of methylating bacteria, dissolved oxygen levels, and the interaction of mercury with dissolved organic matter (DOM). Consequently, a significant portion of mercury contamination originating from human activities, which had previously settled in sediments, is reintroduced into the water column, primarily in the form of highly toxic organic mercury compounds like methylmercury and dimethylmercury. This phenomenon is particularly pronounced in the shallow coastal waters of industrialized regions across the globe. Naturally occurring phytoplankton serve as the primary entry point for these highly toxic mercury forms into the aquatic food web. The availability of mercury, its uptake by phytoplankton, its impact on population size, cell toxicity, subsequent biotransformation, and intracellular stability within phytoplankton are of paramount importance for human health. It is important to note that the mercury sequestered inside phytoplankton cells, owing to biomagnification effects, eventually finds its way into aquatic wildlife, fish, seafood, and ultimately, the human diet. This review aims to provide an overview of recent findings on the interaction between organic mercury forms and natural phytoplankton. Additionally, it offers fresh insights into this intricate relationship and suggests potential directions for future research, with a focus on preventing mercury biomagnification considering scenarios involving climate change and increasing global pollution.