As requested I'm turning my Comment into an Answer.
These look like classic water stains to me. The end grain of wood is likened to the open ends of a bundle of straws and can absorb moisture like a sponge which is why stains can run so deep.
Note that if the staining runs very deeply indeed say 4" (10cm) or more, or clearly progressing down through the longitudinal grain (which isn't absorbent) it is from fungal activity.
Is this a temporary condition?
The colour change is usually permanent (as in it won't go away on its own or fade from sunlight exposure).
It is possibly treatable with certain kinds of wood bleach though. If the stains are due to iron in the water good results should be achieved using oxalic acid which is the classic treatment for this type of staining:
Source: Repair a Water-Damaged Finish on Popular Woodworking.
Does it cause any problems working with it?
If it's just staining the wood won't be any different that you'd notice. With many woods however if water is in contact with it for a long time (either in one go or through repeated wetting cycles) decay can set in, but staining will often occur a long time before decay starts.
It's hard to tell for sure from the photo but the wood looks sound so this could merely be a cosmetic issue. If not the soft earlywood (the pale parts of the grain) will be softer than normal, noticeably spongy or 'punky'.