The marine shells were not produced away from the sea.

As to those who say that shells existed for a long time and were born at a distance from the sea, from the nature of the place and of the cycles, which can influence a place to produce such creatures—to them it may be answered: such an influence could not place the animals all on one line, except those of the same sort and age; and not the old with the young, nor some with an operculum and others without their operculum, nor some broken and others whole, nor some filled with sea-sand and large and small fragments of other shells inside the whole shells which remained open; nor the claws of crabs without the rest of their bodies; nor the shells of other species stuck on to them like animals which have moved about on them; since the traces of their track still remain, on the outside, after the manner of worms in the wood which they ate into. Nor would there be found among them the bones and teeth of fish which some call arrows and others serpents’ tongues, nor would so many [Footnote: I. Scilla argued against this hypothesis, which was still accepted in his days; see: La vana Speculazione, Napoli 1670.] portions of various animals be found all together if they had not been thrown on the sea shore. And the deluge cannot have carried them there, because things that are heavier than water do not float on the water. But these things could not be at so great a height if they had not been carried there by the water, such a thing being impossible from their weight. In places where the valleys have not been filled with salt sea water shells are never to be seen; as is plainly visible in the great valley of the Arno above Gonfolina; a rock formerly united to Monte Albano, in the form of a very high bank which kept the river pent up, in such a way that before it could flow into the sea, which was afterwards at its foot, it formed two great lakes; of which the first was where we now see the city of Florence together with Prato and Pistoia, and Monte Albano. It followed the rest of its bank as far as where Serravalle now stands. >From the Val d’Arno upwards, as far as Arezzo, another lake was formed, which discharged its waters into the former lake. It was closed at about the spot where now we see Girone, and occupied the whole of that valley above for a distance of 40 miles in length. This valley received on its bottom all the soil brought down by the turbid waters. And this is still to be seen at the foot of Prato Magno; it there lies very high where the rivers have not worn it away. Across this land are to be seen the deep cuts of the rivers that have passed there, falling from the great mountain of Prato Magno; in these cuts there are no vestiges of any shells or of marine soil. This lake was joined with that of Perugia [Footnote: See PI. CXIII.]

A great quantity of shells are to be seen where the rivers flow into the sea, because on such shores the waters are not so salt owing to the admixture of the fresh water, which is poured into it. Evidence of this is to be seen where, of old, the Appenines poured their rivers into the Adriatic sea; for there in most places great quantities of shells are to be found, among the mountains, together with bluish marine clay; and all the rocks which are torn off in such places are full of shells. The same may be observed to have been done by the Arno when it fell from the rock of Gonfolina into the sea, which was not so very far below; for at that time it was higher than the top of San Miniato al Tedesco, since at the highest summit of this the shores may be seen full of shells and oysters within its flanks. The shells did not extend towards Val di Nievole, because the fresh waters of the Arno did not extend so far.

That the shells were not carried away from the sea by the deluge, because the waters which came from the earth although they drew the sea towards the earth, were those which struck its depths; because the water which goes down from the earth, has a stronger current than that of the sea, and in consequence is more powerful, and it enters beneath the sea water and stirs the depths and carries with it all sorts of movable objects which are to be found in the earth, such as the above-mentioned shells and other similar things. And in proportion as the water which comes from the land is muddier than sea water it is stronger and heavier than this; therefore I see no way of getting the said shells so far in land, unless they had been born there. If you were to tell me that the river Loire [Footnote: Leonardo has written Era instead of Loera or Loira—perhaps under the mistaken idea that Lo was an article.],which traverses France covers when the sea rises more than eighty miles of country, because it is a district of vast plains, and the sea rises about 20 braccia, and shells are found in this plain at the distance of 80 miles from the sea; here I answer that the flow and ebb in our Mediterranean Sea does not vary so much; for at Genoa it does not rise at all, and at Venice but little, and very little in Africa; and where it varies little it covers but little of the country.

The course of the water of a river always rises higher in a place where the current is impeded; it behaves as it does where it is reduced in width to pass under the arches of a bridge.

Taken from The Notebooks of Leonardo da Vinci edited by Jean Paul Richter, 1880.

Notebooks of Leonoardo da Vinci
XVI: Physical Geography.
. . .
On the way in which the sources of rivers are fed.
The tide in estuaries.
On the alterations in the channels of rivers.
The origin of the sand in rivers.
The formation of mountains.
The authorities for the study of the structure of the earth.
Doubts about the deluge.
That marine shells could not go up the mountains.
The marine shells were not produced away from the sea.
Further researches.
Other problems.
Constituents of the atmosphere.
On the motion of air.
The globe an organism.
. . .