The deep-water wharf that will serve as a refuelling hub for Canadian sovereignty patrols in the Arctic is slowly sinking for reasons that only became apparent several years after Ottawa announced Nanisivik would be this country's northernmost naval facility.

In 2010, measurements showed the Baffin Island wharf had sunk about two metres since construction in the mid-1970s. Engineers went "searching for plausible ways to explain why the structure had settled so much," says a technical paper on the matter presented to a 2013 civil engineering conference in Alaska.

In 2011, exploratory drilling at Nanisivik – 700 kilometres north of the Arctic Circle – discovered a surprise: a deep layer of clay far below the wharf. The clay is believed to be compressing, which would account for the sinking.

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"Survey results and 2011 geotechnical investigations revealed the stability of the wharf is in question," says the engineering paper, Stability Challenge for a Wharf in the High Arctic, whose authors include a Department of National Defence employee.

The stability problem facing Nanisivik wharf raises questions about its suitability as a naval facility and suggest the Canadian government could be facing big bills to address the matter.

DND says it cannot say whether the wharf is settling at a slow and steady rate, or an increasing rate, because it lacks sufficient accurate data.

The settling is among the reasons why the military scaled back plans for upgrading Nanisivik wharf, which in 2007 Prime Minister Stephen Harper made a keystone of his strategy for increasing Canada's presence in the Far North. The facility will offer yet-to-be-built Arctic patrol ships a northern filling station so the Royal Canadian Navy can make extended visits to the region.

Engineers have since warned against adding a lot of weight to the dock as part of a refurbishment unless action was taken to stabilize it. "Scenarios that add load will likely result in accelerated movement of the structure," the engineering paper says.

DND is playing down the risk to the wharf. Rodney Watson, a department spokesman and one of the authors of the 2013 engineering paper, said the military doesn't believe the problem will affect operations. The first Arctic patrol ships are expected to begin operations in the 2019 summer shipping season.

"I think sinking is probably not the word we would use for that. That sounds a little dramatic," he said. "There's absolutely no impact on the intended function of the site or planned use of the facility."

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He said experts consulted by DND think the majority of the settling took place between 1975 and 2000, the first 25 years after the wharf was constructed. Nearby mining operations ceased in 2002.

The 2013 paper on Nanisivik, however, says experts lack enough information to discern how fast the wharf is sinking or what stage of settlement it has reached. "The data are insufficient to determine whether the soils are in primary, secondary or tertiary (approaching failure) creep," it says, referring to downward movement.

A bigger refurbishment of Nanisivik was scaled back in 2012 because of cash constraints. DND's budget for the project remains the same but it ratcheted back redevelopment because plans proved more expensive than expected.

A major redo of the wharf that would have used a lot of cement is also shelved. DND had considered renovating the jetty, which consists of three, separate circular docks, by filling in the area between them.

DND says it will keep monitoring the wharf "until we get a better understanding of the conditions of the soil."

One option to reduce settlement would be using devices called thermosyphons to make the surrounding ground even colder. Mr. Watson says this would be very costly. Another option – not one DND has mentioned – would be building a new wharf. Mr. Watson says that would be "very, very expensive."

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Asked how long the wharf is rated for in its current state, National Defence officials said it was determined the wharf would "certainly last" for 15 to 20 years, using 2011 as the start date. By 2019, when the new Arctic patrol ships are expected to begin summer operations, this life expectancy will have dropped to seven to 13 years.