Under your settings, the bibliography is printed as a \section, which naturally updates the header content using \markboth. You can set \markboth to gobble its arguments temporarily, which would therefore not affect the header:
{\renewcommand{\markboth}[2]{}% Remove header adjustment\printbibliography}Here is your minimal example:
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\documentclass[twocolumn]{article}\usepackage[style=authoryear,maxcitenames = 2,mincitenames = 1,maxbibnames = 99,minbibnames = 1,dashed = false,firstinits=true,backend=biber]{biblatex} % !BIB TS-program = biber %^ line above is necessary to tell TeXShop to use Biblatex rathern than traditional BibTex.\usepackage[utf8]{inputenc} % utf8 support \usepackage[T1]{fontenc} % code for pdf file % w/out these two lines, I get the warning, "WARN - The entry '_______' has characters which cannot be encoded in 'ascii'. Recoding problematic characters into macros.\usepackage{fancyhdr}\usepackage{filecontents}\begin{filecontents}{Test.bib} @unpublished{usgs_gmted_data,Author = {{United States Geological Survey}},Title = {USGS Global Multi-resolution Terrain Elevation Data (GMTED) product},Url = {http://topotools.cr.usgs.gov/gmted_viewer/},urldate = {2013-09-01}, urlmonth = {September}, Year = {2010}}\end{filecontents}\addbibresource{Test.bib}\renewcommand\headrulewidth{0pt} % No line under running header\pagestyle{fancy}\rhead[R]{my running header}\begin{document}abc\newpage\nocite{*}\newpageabc{\renewcommand{\markboth}[2]{}% Remove header adjustment\printbibliography}\newpageabc\end{document} 