The Sea Mammal Research Unit (SMRU) at the University of St Andrews will conduct the three-year study.
Marine scientists will attach telemetry tags harmlessly to the fur at the back of the heads of a number of seals.
The scientists said the tags were lightweight and would drop off when the seals moulted.
The marine tags, which work in a similar way to smartphones, will use technology to send vital information from the seal when it surfaces or beaches directly back to SMRU for analysis.
The technology, provided by Vodafone, is the same as that which is found in new cars, heart monitors and smart meters.
Data will be gathered on a seals' location, dive behaviour and its oceanic environment.
The study by SMRU is being carried out at the request of the Scottish government and Scottish Natural Heritage which have concerns for the future survival of harbour seals in areas of Scotland.
Harbour seals - one of two seal species in the UK - have declined in numbers by up to 90% in some areas in and around the north and east coast of Scotland, including Orkney, since 2000.
Professor John Baxter, marine principal adviser at Scottish Natural Heritage said: "This exciting, collaborative study is vital to help us to better understand the drivers of population change in Scottish harbour seals, and to evaluate the potential conservation and management options open to us."
SMRU's deputy director Dr Bernie McConnell said: "Over the last 15 years, many of the harbour seal populations in the Northern Isles and on the north and east coasts of Scotland have been declining.
"Marine data collected during this project on Orkney will help to assess the causes, management and mitigation options in relation to the harbour seals decline and to prioritise future research directions."
Orkney seals are to receive mobile smartphone technology as part of a study into population decline in the area.