Begins with future miners (digging up old rubbish tips looking to reclaim minerals from disposable nappies) finding a body, during the investigation, another body is discovered, then more, eventually millions of bodies are uncovered and the terrible truth is uncovered!

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    What is the terrible truth? You can use the spoiler tags to hide it if that's your worry, but if there's a big twist or reveal, that will probably help people find the story you're looking for. – Vanguard3000 May 20 '18 at 20:13
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    @Vanguard3000 there actually isn't a revelation, except that the truth must be terrible given the number of skeletons. Several eerie possibilities are considered by the narrator to explain the skeletons and other weird occurrences, such as people asking to stop digging without remembering having done so, or knowing why. – LSerni May 20 '18 at 21:06

It is a short story by David Brin, Detritus Affected.

Future miners (archaeologists with industrial backing) digging old rubbish (and diapers):

Tried angling stories about disease germs, festering in the dump along with five billion ancient disposable diapers

Keoki pays the freight, testing rich veins of complex organics and heavy metals for our industrial sponsor. It's a long shot, but if the assay proves out, Fabrique Chang may bid to come mine Hyperion. One generation's junk can be the next's mother lode.

They find one skeleton

Zola found the bones down at South-22, a neat row of ribs sticking through a pile of dingy rags. At first we thought it was a pet, some large dog. On realizing they were human, we had no choice but to report it. We're digging in strata from A.D. 1958, after all. It might be somebody's long-missing great-uncle.

...then more.

Today's big discovery—this time at South-31—four more sets of bones.

and more.

A million skeletons so far, with no end in sight. Reports come in from other cities. Of landfill boneyards in New York, Atlanta, Seattle . . . though none as extensive or dating so far back as Los Angeles. Perhaps that means it happened first and most profoundly here, in L.A.

But what? What happened here? Whence came the dead?

Ending explained in the spoiler block.

The archaeologists also receive threats telling them to stop digging. These are tracked down to people in care homes. The implication is that these are alien invaders who successfully killed and replaced the original humans back in 1958. There are other possibilities considered, but that seems the most plausible. However the narrator would prefer almost anything else.

  • Based on the very end of the story I got the impression that all of the bodies were people who wanted a slower pace of life and just sat around watching the trees grow until they died. – Xantec Jun 18 '18 at 0:49

While Detritus Affected strongly matches the majority of the details in the original question, as indicated in this answer, the plot element

reclaim ... from disposable nappies

suggests that the original poster might also be remembering details from Planet of the Sealies, where the diapers were actually of interest for

the genetic information they contain.

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