The gooey, clear discs are abundant in the water or along the shores of the bay. They are marked with a distinct white X or cross, and there are reports of them gumming up the netting of herring weirs.
Nick Record, a senior research scientist at Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine, is building a library of jellyfish sightings based on citizen reports.
He said reports of white cross jellyfish started coming in about two weeks ago, first in Penobscot Bay in Maine and then in the Bay of Fundy.
"Over the last week or so, reports have been coming in of just very high densities of white cross jellies," said Record.
He said there have been reports of white cross jellies along the coast from the Bay of Fundy to Boston as far back as the 1800s, but there is no baseline research on them in the area.
"They are not new to the region, but then there will be long periods of time where nobody reports any and then they'll suddenly show up again," he said.
"Part of it is cyclical, but without baseline scientific data, it's really hard to say how common these sort of cycles typically are or how abundant they become."
Record said spikes in the population of jellyfish have been seen in places such as the Sea of Japan, the Black Sea and inland bays and estuaries, such as Cheasapeake Bay in the United States.
The senior research scientist at the Bigelow laboratory says a theory he calls "the jelly ocean hypothesis" is circulating among scientists, who say "we are actually shifting toward an ocean that is more favourable to gelatinous zooplankton, which is kind of the general name for jellyfish and jellyfish-like organisms."
Record said scientists across the globe are questioning whether the rise in jellyfish population is cyclical or whether it is a global shift.
"Both of those sides of the debate right now you'll find in the scientific literature. This is one of those issues that is not settled in science," he said.
Record said the hypotheses as to why jellyfish blooms happen mostly relate to human activities, ocean warming or fertilizer runoff into the oceans.
"There are a lof of potential causes, and it could be that these different factors are all operating in different places of the world, but because there is a lot of human activity in general you find a lot of things shifting to favour jellyfish," he said.
"Other scientists will say this is just part of a natural 20- to 30-year cycle, and the jellyfish will come, and indeed they will go."
In his efforts to establish a database of jellyfish sightings in the Gulf of Maine and Bay of Fundy, Record is asking anyone with who spots a jellyfish to note the location, time, description and take a photograph if possible.
The information can then be sent to him at email@example.com or tweeted with the hashtag #mainejellies.