JF Ptak Science Books Post 2214
"The whole of the river was an opaque pale brown fluid. ....... surely the river which flows for so many miles through London ought not to be allowed to become a fermenting sewer." --Michael Faraday
The Thames evidently was all of that, and much more.--but its biography became all the more explicit in the 19th century when people took a very close look at samples of its water with microscopes. The result was outrage and heaped disgust.
There is a much-quoted quote from Charles Dickens, spread around the internet, but offered everywhere without attribution, offering up the River Thames as 'a dank, stinking sludge, the scene of murders and crime'. Another (attributed) bit of Dickens celebrating the horribleness of the river goes further: "Miles of close wells and pits of houses, where the inhabitants gasped for air, stretched far away towards every point of the compass. Through the heart of the town a deadly sewer ebbed and flowed, in the place of a fine fresh river."--(Little Dorrit, Cbook I chapter 3) I don't know if Dickens ever saw samples of the river water, and so far as I can tell he didn't write about it, though perhaps he didn't need to--the macroscopic level of the river was more-than-enough for him.

[Image source: the Wellcome Collection, following an image-post by Jennifer Ouellette]
It is unknown to me how early published images get to be illustrating the microscopic world of the Thames, but as we can see above in William Heath's 1828 hand-colored etching, the realization of the endless varieties of constellations dislocated any warm/fuzzy feelings that Londoners would have harbored regarding their river.
Here's another example of discovery, appearing in the much-read Punch, or the London Charivari (a satirical, sharp and biting magazine based on the earlier French periodical Le Charivari which began publishing in 1832) in 1850:
The caption reads in part: "And wondrous indeed is the scene disclosed within the sphere of a little drop of water of that water which Londoners drink swallowing daily myriade and myriads of worlds whole universes instinct with life or life in death."
There's so much that can be written about the river and the stink and cholera and the general nastiness and healthy aspects of using it for human consumption, and of understanding epidemics and their transmission of disease and sanitation and flush toilet impact and so on, in addition to its general moral decay and criminality...but that will have to wait for some other time. The 1840's and 1850's and Dickensian London was a Big Time for the Thames, and not in a good way. It was an effluent life-force of the city that was spiked with disease and terror, reaching a high/low exclamation in the cholera epidemic of 1854.
But there were many low points for the river in those decades, and Dickens (since I've been quoting him here) was a major proponent of sanitary engineering for London, writing (particularly in his newly-established literary journal, Household Words, begun in 1850) and frequently speaking on the topic. He was a major public figure, and his words were influential and reached a vast audience. Still the improvement of the river took decades, and its miasmic mess reached well into the 20th century, and was declared basically biologically dead int he 1950's, though it has rebounded today into being one of the world's cleanest rivers coursing through a city.
Here's another nightmarish vision of the river by Dickens, this from David Copperfield: "The neighbourhood was a dreary one at that time; as oppressive, sad, and solitary by night, as any about London. There were neither wharves nor houses on the melancholy waste of road near the great blank Prison. A sluggish ditch deposited its mud at the prison walls. Coarse grass and rank weeds straggled over all the marshy land in the vicinity. In one part, carcases of houses, inauspiciously begun and never finished, rotted away. In another, the ground was cumbered with rusty iron monsters of steam-boilers, wheels, cranks, pipes, furnaces, paddles, anchors, diving-bells, windmill-sails, and I know not what strange objects, accumulated by some speculator, and grovelling in the dust, underneath which — having sunk into the soil of their own weight in wet weather — they had the appearance of vainly trying to hide themselves. The clash and glare of sundry fiery Works upon the river-side, arose by night to disturb everything except the heavy and unbroken smoke that poured out of their chimneys. Slimy gaps and causeways, winding among old wooden piles, with a sickly substance clinging to the latter, like green hair, and the rags of last year's handbills offering rewards for drowned men fluttering above high-water mark, led down through the ooze and slush to the ebb-tide. There was a story that one of the pits dug for the dead in the time of the Great Plague was hereabout; and a blighting influence seemed to have proceeded from it over the whole place. Or else it looked as if it had gradually decomposed into that nightmare condition, out of the overflowings of the polluted stream.--David Copperfield, 1850, chapter 46. Courtesy of the World Digital Library: http://www.wdl.org/en/item/3956/zoom/