A large fraction of mercury contaminant in the environment is from industrial production, and it potentially impairs human health once entering the food chain. Millions of people reside in the Pearl River Delta region, and water quality in the estuary directly affects their drinking water safety. Considering the highly intense anthropogenic activities and industrial productions, we attempted to measure the sediment mercury concentration in the Pearl River estuary. In this work, samples of a creek sediment within this region were collected and mercury concentrations were quantified. Total mercury, simultaneously extracted mercury, methylmercury, and bio-accumulated mercury were individually assayed. Results indicated that total mercury concentrations of investigated sites ranged from 1.073 to 4.450 µg/g dry sediment. The mercury in the sediment also transformed into more toxic methylmercury, which then adversely affected benthos biodiversity. Correlation analysis revealed that, mercury was accumulated into benthic microorganisms, mainly through the uptake of methylmercury. High concentrations of acid-volatile sulfide in the sediment indicated the presence of active sulfate-reducing bacteria, which could also catalytically transform inorganic mercury into methylmercury. Correlation analysis further showed that sulfate-reducing bacteria activity accounted for methylmercury formation.