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The meridional overturning circulation (MOC) has been measured by boundary arrays in the Atlantic since 2000. Over the past decade of measurements, however, the reported tendencies in overturning circulation strength have differed between 16°N and 26°N. Here we investigate these differences by diagnosing their origin in the observed hydrography, finding that both arrays show deep waters (below 1,100 dbar) at the western boundary becoming fresher and less dense. The associated change in geopotential thickness is about 0.15 m2 s−2 between 2004–2009 and 2010–2014, with the shift occurring between 2009 and 2010 and earlier at 26°N than 16°N. In the absence of a similar density change on the east of the Atlantic, this middepth reduction in water density at the west would drive an increase in the shear between the upper and lower layers of North Atlantic Deep Water of about 2.6 Sv at 26°N and 3.9 Sv at 16°N. These transport anomalies result in an intensifying tendency in the MOC estimate at 16°N, but at 26°N, the method of correcting the geostrophic reference level results in an opposing (reducing) tendency of the MOC. The results indicate that both arrays are observing coherent, low‐frequency changes, but that there remain discrepancies in the methods of addressing the geostrophic reference level for boundary arrays measuring ocean circulation.