By bus
Wakura Onsen's diminutive but centrally located bus terminal offers frequent services to Nanao ¥350, 20 min and occasional services to Kanazawa ¥2300 and Anamizu.
By train
Wakura Onsen is the terminus of the JR Noto Line, which connects from Kanazawa and Tsubata on the JR Hokuriku Main Line. However, only limited expresses from Tokyo, Osaka and Nagoya go all the way; all ordinary JR services terminate at Nanao, one stop down the line, from where you'll have to wait for a connecting Noto Railway train ¥180, roughly hourly or take a bus ¥350, every half hour or so. You can also use the Noto Railway to come in from Anamizu to the north.
All that said, the train station is actually located a rather inconvenient 3 km out of town. Many ryokan offer pickup/dropoff services, or you can wait for the buses from Nanao which stop at the station on their way into town.
By plane
Noto Airport is a 40-min shared taxi ride away ¥1100.