In the beginning of the story, Holmes senses that Helen has been frightened into a state of nervous exhaustion.  She looks terrible.  Her emotional state has made her old before her time. 

"Her features and figure were those of a woman of thirty, but her hair was shot with premature gray, and her expression was weary and haggard.
Sherlock Holmes ran her over with one of his quick, all-comprehensive glances." (Doyle)

Then Holmes notices something else about Helen Stoner, something that is very disturbing, he sees evidence of physical abuse as well.  He asks her about her bruised wrist, which indicates that her stepfather, Dr. Roylott has gotten physically violent with her.  

"You have been cruelly used," said Holmes.   The lady coloured deeply and covered over her injured wrist.  "He is a hard man," she said, "and perhaps he hardly knows his own strength." (Doyle)