Researchers found that extra rainfall drives up the amount of organic material flowing into the seas.
This alters the food chain, adding another layer of complex organisms which boosts the concentrations of mercury up the line.
According to the World Health Organisation, mercury is one of the top ten threats to public health.
The substance at high levels has been linked to damage to the nervous system, paralysis and mental impairment in children.
Scientists recreated the conditions found in the Bothnian sea estuary. They discovered that as temperatures increase, there is an increased run-off of organic matter into the world's oceans and lakes.
This encourages the growth of bacteria at the expense of phytoplankton.
"When bacteria become abundant in the water there is also a growth of a new type of predators that feed on bacteria," lead author Erik Bjorn from Umea University in Sweden.
Levels of mercury in the world's ecosystems have increased by between 200 and 500 per cent, since the industrial revolution, driven up by the use of fossil fuels such as coal.
The study suggests that climate change may be driving up levels of methylmercury in a manner not previously recognised.
The study was published in the journal Science Advances.
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