Nioghalvfjerdsfjorden Glacier (N79) is one of the two main outlets for Greenland’s largest ice stream, the Northeast Greenland Ice Stream (NEGIS), and is the more stable of the two, with no calving front retreat expected in the near future. Using a novel elevation reconstruction approach combining digital elevation models (DEMs) and laser altimetry, previously undetected local phenomena are identified complicating this assessment. N79 is found to have a complex network of basal channels that were largely stable between 1978 and 2012. Since then, an along-flow central basal channel has been growing rapidly, likely due to increased runoff and ocean temperatures, and possibly threatening to decouple the glacier’s northwestern and southeastern halves.