Healey and Woodall were not able to analyze any sediments underneath more than one meter (3.3 ft) of water because the particles were too fine for the Ekman dredge sifter that they used. In 2013 Sarah Shenstone-Harris, a University of Toronto undergraduate interning at the schools Centre for Global Climate Science, was able to analyze the sediments. She looked to the diatoms in them to try to see if climate change had played a role in the lakes decline. If so, she also asked, when did that change occur, and was it possible to restore the lake to a level of water quality comparable to what it had been prior to the establishment of Yellowknife?
Shenstone-Harris started from the observation that subarctic lakes generally had shown great sensitivity to climate change because of shifts in the amount of ice cover. Those stresses could be exacerbated for subarctic lakes in an urban area facing higher levels of pollution from a number of different sources, such as Frame. Her inquiry was a paleolimnological one, focusing on the algae species present in the lake at various times in the recent past. She took core samples of the sediment down to  and dated them by the lead-210 levels. Once their age was established, she looked at the diatom remains, since the species of algae in the water can reflect environmental changes, and counted the ratio of chrysophyte stomatocysts to establish nutrient levels in the water at that time.
Due to diatom dissolution at the lowest level of the sediments taken, Shenstone-Harris was unable to establish data for any years earlier than 1943, making it impossible to set the desired baseline for a pre-settlement Frame Lake. However, she was able to establish that the lake had always been at a high trophic state, even before it became fully eutrophied by the mid- to late-1990s. That was preceded by a rapid replacement of epiphytic species with benthic ones around 1990.
It was not clear to Shenstone-Harris that that event had been the result of climate change. From 1956 to 1992, the last year records were kept, ice cover on the lake remained relatively stable throughout the winter, yet the amount of Cyclotella and Fragliaria, two genera whose species have been shown to be responsive to changing ice cover and warming climates, varied considerably. This suggested to her that while climate change may be a factor in the lakes decline, it is not the only one. Instead, the change in species around 1990 pointed to a change in littoral zone microhabitat, a loss of macrophytes and mosses, as bearing the primary responsibility for tipping the lake to its present eutrophic state. However, the lack of data on ice cover since 1992 and her inability to determine the lakes status prior to the establishment of Yellowknife qualified that conclusion. "Alternatively", she wrote, "Frame Lake may be a subarctic anomaly and was always high in nutrients".
In 2015 the Carleton team was able to examine the sediments. They found that the period between the late 1940s and 1970 added a half-meter () of sediment to the bottom of the lake, the most of any lake in the region. Above it, the  of sediment postdating the causeway was "black, sulfurous smelling and characterized by very high levels of metals, particularly arsenic". These are consistent with the patches of sediment Mallon recalled from his youthful recreation on the lake in his 2015 article, noting that "I can still vividly feel the stuff's gloopy embrace on my feet" (although an accompanying sidebar by another reporter suggested that the sediments may be the result of sewage back-flushed from Niven Lake).