Arcellacea (testate lobose amoebae) were examined in 24 sediment-water interface samples collected over two late August field seasons in 2010 and 2011, from James and Granite lakes, Temagami Region, Northeastern Ontario. The work was carried out to quantitatively test species-environment relationships in a lake system known to be characterized by a significant pH gradient, partially the result of contamination from the early twentieth century Northland Pyrite Mine Co., located on the shoreline in the southern basin of James Lake. Redundancy analysis confirmed that arcellacean assemblage structure was most strongly controlled by pH, explaining 14.06 % (p < 0.002) of the total variance. Q- and R-mode cluster analysis supported by detrended correspondence analysis yielded two major faunal assemblages. The Oligotrophic Assemblage (1) had a Shannon Diversity Index (SDI) ranging up to 2.45, typical of healthy boreal lakes. This assemblage characterized samples collected from higher pH stations within James and Granite lakes away from the immediate area of the mine site, while the Low pH Assemblage 2010 (2a) and Low pH Assemblage 2011 (2b) groupings were from the very low pH environments of James Lake adjacent to the former mine site. Both low diversity assemblages (SDI ranging from 0.62 to 1.22) were characterized by Arcella vulgaris, a species known to thrive in hostile lacustrine environments. Differing depositional conditions during August 2010, a probable result of different prevailing wind patterns that summer, led to allochthonous specimens of the seasonally planktic Cucurbitella tricuspis dominating the Low pH Assemblage 2010 (2a) fauna.