From the sailors in the opium dens of Limehouse to the smugglers on the malarial flats of the estuary, ...
What does "Malarial flats" mean?
malarial flats = flat areas where it's easy to contract malaria
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AHD "flat" n., def. 2. "2. often flats A stretch of level ground: salt flats.
The Thames has mudflats at low tide. "Malarial" actually refers to the disease malaria, which was apparently indigenous to England back then. The disease is carried by the mosquitoes that breed in the standing water you find near rivers, so the flats were malarial.
Flats are low-lying land areas near the sea. These lands can be covered with standing, stagnant fresh or seawater. Mosquitoes that carry malaria can rapidly and easily reproduce in areas like this. People who live there are frequently infected and can die from the disease.