Qualifications
Since a limnologist is part wildlife biologist, part chemist, part ecologist, part environmental scientist, part hydrologist, and even part fisheries biologist, you can get a bachelor of science degree in biology, ecology, chemistry, physics, geology, or even math.
But after that…
Most employers require that limnologists (no matter what their specialty) have a master's or even doctorate degree that indicates their specialty. Some schools offer master's and doctor degrees in limnology and some don't. You'll have to poke around a bit to see what fits your desired area of specialty (source).
But even before you start college, take a bunch of high school classes in upper science and math, and figure out a way to work at—or even volunteer for—science museums, aquariums, or nature groups. A little experience can go a long way.
Even after college, before graduate school, many people opting to delve into limnology choose to get some hands-on experience such as participating in a research project, talking to school children, and even leading a camp for kids interested in the water sciences.
As you can see, limnology and related water sciences are immersive, and a broad education is necessary to be successful.