Navas has helped Los Blancos win one La Liga title and three Champions League crowns over the last three seasons, but the Costa Rican's spot as number one is now under threat from Courtois.
Courtois arrived at Madrid from Chelsea last week, and the Belgium international is widely expected to be handed the gloves for the 2018-19 campaign.
Lopetegui, however, has insisted that he does not see the dilemma as a selection headache.
"Keylor and Courtois? We have huge competition for places, and that's good for the team," Lopetegui told reporters.
"There'll always be a problem, regardless of what decision we make, because there will always be a goalkeeper who doesn't play, but we don't see it as a problem, rather as two magnificent solutions."
The Champions League winners will take on Europa League holders Atletico Madrid in the UEFA Super Cup on Wednesday night.