Ana Monteiro qualified ninth out of 33 swimmers with a time of 2:09,43 minutes.
Alexis Santos and Gabriel Lopes qualified for the semi-finals to take place on Tuesday in the 200m medley, with 1:59,01 and 1:59,76 respectively.
Santos was fourth in his heat, with the 10th best qualifying time, while Lopes finished sixth in his heat, with the 16th best time out of 51 participants.
In the 100m freestyle, Miguel Nascimento went out in the qualifiers, with the 44th time (49.98 seconds).
Monteiro's semi is on Wednesday, at 9.10 p.m. local time (1.10 p.m. in Lisbon), just before Santos and Lopes compete in their semi.
On Thursday, Lopes is to compete in the 200m backstroke, and Victoria Kaminskaya in the 200m breaststroke.