Arcellinida (testate lobose amoebae) were examined from 22 surface-sediment samples collected from homogenous environments in eastern Canadian lakes (Lac du Castor Blanc, SW Quebec; Oromocto Lake, SW New Brunswick) to: 1) evaluate the faunal consistency of assemblages within the targeted environments; and, 2) assess the Arcellinida assemblage response evident in samples collected from Oromocto Lake in 2010 CE (n = 10) and 2012 CE (n = 6) to inter-annual changes in environmental conditions. Cluster analysis and detrended correspondence analysis (DCA), redundancy analysis (RDA), and Bray-Curtis Dissimilarity Matrix (BCDM) were used to identify the dominant arcellinidan assemblages, determine physicochemical controls over the Arcellinida distribution, and assess the assemblages’ faunal homogeneity, respectively. Cluster analysis, DCA, and BCDM results revealed two distinct and relatively homogenous arcellinidan assemblages: 1) Lac du Castor Blanc Assemblage; and 2) Oromocto Lake Assemblage, which could further be subdivided into Oromocto Lake 2010 CE (OL10), and 2012 CE (OL12) sub-assemblages. RDA results showed that 65.6% of the variance in the arcellinidan distribution could be attributed to four significant parameters; sand size fraction (32.1%), calcium (29.2%), manganese (2.7%), and organic content (1.5%). The OL10 and OL12 sub-assemblages aligned well with the respective sample collection dates of 2010 CE and 2012 CE, with proportions of the healthy-lake-indicating Diffluggiid taxa being higher in OL12, likely due to a concurrent slight increase in substrate organic content in the 2012 CE sediments. Our results confirm the faunal homogeneity of assemblages in limnologically similar environments, and demonstrate the rapid response of Arcellinida assemblages to changes in lake conditions at inter-annual time scales.