In addition, low estrogen levels can adversely affect the vagina, causing thinning of the walls and dryness, which can lead to painful sex. The lining of the urethra also thins, leaving the body susceptible to infections like UTIs. Symptoms of low estrogen may include: 1  Fatigue. 2  Hot flashes. 3  Night sweats. 4  Memory lapses. 5  Difficult concentrating. 6  Joint pain. 7  Vaginal dryness. 8  Dry skin (which can lead to premature aging, wrinkles, and brown age spots).