Jessika:
There is a brief discussion of deposition in wells on p. 134 of Cleary's "Putting the Dead in Their Place: burial Location in Roman Britain" in the book Burial, Society and Context in the Roman World ( readable online).
Also, I might have written a little bit about layers in a well in a medieval/post-medieval house in Northeim, Germany that had masses of botanical remains. I don't currently have access to my article, but it is "Muehlsteinreste aus einem frühneuzeitlichen Brunnen im Beriech des Entenmarktes in Northeim," Northeimer Jahrbuch 56:78-95 (1991). Maybe one of the other articles in the journal on the well in the Engenmarkt has useful material. In any case, my notes detailing the layering as much as I could should still be in the Northeim Heimatsmuseum.
This title is suggestive: Reitz, E. J. "The wells of Spanish Florida: Using taphonomy to identify site history." Journal of Ethnobiology 14, no. 1 (1994): 141-160.
Link, Thomas, Dirk Schimmelpfennig, and Fokus Jungsteinzeit Berichte der AG Neolithikum. "2 Sinn und Zweck" (https://www.sciencedirect.com/science/article/pii/S0031018206003853) specifically discusses wells and taphonomy.
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