Scaphoid fractures are diagnosed based on clinical examination findings, and imaging. It is usually tender to push over the anatomic snuffbox on the thumb side of the back of the wrist, and it may be tender when the thumb is telescoped. These findings would prompt further investigations in the form of x-rays, CT scans or MRI scans.
X-rays are a good starting point, but they might miss subtle fractures of the scaphoid because it is a 3D bone and the x-rays take images in 2D. The next step is usually a CT scan or an MRI scan. CT is very good at picking up fractures, and helps plan surgery if this is needed. But CT might miss the occasional fracture, and can't rule out ligament injuries of the wrist. MRI has the advantage of an extremely high pick up rate, and the ability to detect ligament injuries too.
For more info see:-
Scaphoid fractures – Rupert Wharton
References:-
Davis TRC Ann R Coll Surg Engl 2013; 95: 171–176
doi 10.1308/003588413X13511609956895