The 47-year-old man and 54-year-old woman, from Crawley in West Sussex, were arrested in the town - around five miles from the airport - at about 10pm on Friday.
Sussex Police said the pair are being held on suspicion of “disrupting services of civil aviation aerodrome to endanger or likely to endanger safety of operations or persons”.
Superintendent James Collis said: “Our investigations are still ongoing and our activities at the airport continue to build resilience to detect and mitigate further incursions from drones, by deploying a range of tactics.
“We continue to urge the public, passengers and the wider community around Gatwick to be vigilant and support us by contacting us immediately if they believe they have any information that can help us in bringing those responsible to justice.
“The arrests we have made are a result of our determination to keep the public safe from harm, every line of inquiry will remain open to us until we are confident that we have mitigated further threats to the safety of passengers.”
Meanwhile, Gatwick Airport said on Saturday morning that the runway is open but passengers are urged to check with their airline before travelling.
Around 1,000 flights have been cancelled or diverted since drones were spotted inside the perimeter of the UK’s second biggest airport on Wednesday at around 9pm, affecting approximately 140,000 passengers.
A handful of flights due to arrive into Gatwick on Saturday were cancelled, according to the airport’s website, including an easyJet service from Milan-Linate and a TUI flight from Bridgetown, Barbados.
An airport spokesman said: “Our runway is open and we aim to run a full schedule on Saturday December 22 - 757 flights scheduled today, carrying 124,484 passengers.
“Passengers should expect some delays and cancellations as we continue to recover our operations following three days of disruption and are advised to check with their airline before travelling to the airport.
“Safety is Gatwick’s top priority and we are grateful for passengers’ continued patience as we work to get them to their final destination in time for Christmas.”
Flights were briefly grounded at the airport on Friday evening after a fresh sighting at around 5.10pm, but military measures reassured operators it was safe to reopen the runway shortly afterwards.
Military equipment was used on Friday to stop further drone disruption while a range of tactics are in place if any unmanned aircraft are seen inside the perimeter.
One piece of equipment believed to have been deployed at the airport is the Israeli-developed Drone Dome system, which can detect drones using radar.
It can also jam communications between the drone and its operator, enabling authorities to take control of and land the device.