The first success of SD Lagunak was reaching the 1998 Copa de la Reina final after beating defending champion RCD Espanyol in the semi-finals.

It reached the Superliga in 2003 after topping its group and beating FC Barcelona and Atlético Jiennense in the promotion play-offs.

[4] In 2006 it qualified for the Copa de la Reina for the first time in the Superliga era following Estudiantes Huelva's relegation.

The next year Lagunak won the Group A and beat Atlético Málaga and CD Arguineguín to regain its spot in the premier category.

A three-group, two-stage reform of the top tier was carried out in 2009; Lagunak didn't make it into the 8-team championship group, but qualified for the expanded 2011 Copa de la Reina, where they were defeated by Athletic Bilbao by an 11-1 aggregate.