Bill,
In 1995 I was on the field crew for William & Mary Center for Archaeological Research (WMCAR) at the 18th century Gloucester town site on the present-day campus of the Virginia Institute of Marine Science, where we recovered significant quantities of shell in historic features (don't recall if it was mussel or oyster).  This was right across the York River from Yorktown.  I recall one of the marine biologists who would check out our dig on his way into his office every morning, and he got very interested when he saw the shells we were recovering from 250-year-old features, saying "Could I have a sample?  We don't find them that large anymore".  I imagine the shells would retain some chemical-trace signature of the water quality that could be compared with modern samples(?)
In any case, I left Virginia shortly afterward, but the report is available from WMCAR for $28. 
Their website is: http://web.wm.edu/wmcar/

Here's the description of the report - Technical Report #23

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"Reclaiming a Tidewater Town: Archaeological Survey, Evaluation, and Data Recovery at Sites on the Campus of the Virginia Institute of Marine Science, Gloucester Point, Virginia" by K. E. Stuck, T. F. Higgins III, C. M. Downing, D. W. Linebaugh, and M. W. McCartney, with contributions by G. J. Brown and S. Dean, 1996 viii + 304 pp. 226 figs., 12 tables, 8 appdx (artifact inventory and some faunal data on microfiche). Gloucester Point has been the subject of numerous archaeological investigations over the last two decades. Overlapping historic-period occupations include the abandoned site of Gloucester Town and fortifications from the Revolutionary and Civil wars. Results of survey, evaluation, and data recovery at sites on the campus of the Virginia Institute of Marine Science are detailed in this report. Excavation results from both military and domestic sites are presented. Results from previous work and the current project are synthesized in a sequence of maps illustrating four centuries of settlement at Gloucester Point.
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> -----Original Message-----
> From: HISTORICAL ARCHAEOLOGY [mailto:[log in to unmask]] On Behalf Of Bill
> Sent: Thursday, January 24, 2013 9:06 AM
> To: [log in to unmask]
> Subject: Re: Freshwater mussels on 18th century sites
>
> Recent excavations on an early 18th century site in central Delaware
> recovered some freshwater mussel shells amongst the faunal remains.
> Normally freshwater mussels are associated with Native American sites in
> the Middle Atlantic region.  This presents the possibility of a Native
> American presence or interaction with the European inhabitants of the site
> (circa
> 1720 to 1735).  Several glass seed beads recovered from floatation further
> support this theory.  My question is: Has anyone found freshwater mussel
> shells on non-Native American 18th century sites in the region?
>
> Thanks for your input in advance!
>
> Bill Liebeknecht, MA, RPA
> Principal Investigator
> Hunter Research, Inc.
> Trenton, New Jersey