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It's plausible that the Nile did, in fact, run red as the Bible suggests.
One possible explanation is known as the “burgundy-blood phenomenon”.
First proposed by Greta Hort in the 1950s, the idea suggests that during the reign of Ramesses II (1303 - 1213 BC) the climate of the capital city Pi-Ramesses began to change from a wet and tropical climate to become drier and more desert-like. As the Nile turned from fast-flowing into a slower, muddier river, it may have provided the perfect conditions for millions of flagellates (specifically Euglena sanguinea and Haematoccus pluvalius, according to Hort) to thrive.
These algae could account for more than just the blood-red color of the river, as their toxicity would explain the death of fish mentioned in the Bible, whilst also accounting for the smell.
The algae could also have forced frogs to leave the river (plague two) before dying. With these predators gone, he suggests, insects would have flourished (plagues three and four), which could have led to the disease of livestock (plague five) and boils (plague six). That’s a whole lotta plague for a bit of algae.