The Euskotren route between Bilbao and San Sebastian is very scenic, but it is slow, as Laura noted. Maybe take it one way and do the return by bus. On the Bilbao end the station is quite near the old town, whereas the bus station is quite a walk away (with tram service, though).
Although the Bilbao and San Sebastian residents speak Spanish, for many the native language is Basque/Euskera. Don't expect to be able to decode the Basque signage.
Both Bilbao and San Sebastian have attractive historic districts as well as some very attractive newer buildings. Bilbao has more art; SS has an extremely lively tapas district. I sort of preferred Bilbao, but it's a close call and SS has one heck of an impressive beach.
There are many pretty, smaller cities in that part of Spain, including the interior capital of Vitoria-Gasteiz, the winey hill town of Laguardia, the coastal border town of Hondarribia (with both a fishermen's district and a hilly medieval quarter), and a bunch of picturesque former fishing villages, including but not limited to Bermeo, Lekeitio, Zumaia, Getaria and Zarautz. Visiting just about any of those will take you through some lovely countryside.
You didn't mention what time of year you plan to travel. The Basque Country is cooler and rainier than central and southern Spain.