I always find such questions really upsetting, because it suggests you know that you are already infected. Some STDs are treated with antibiotics and I guess you don't regard this as 'natural' but you must take what works. Don't pleast try to treat a sexually transmitted disease yourself.
These diseases are contagious and serious. You must see a doctor. Bacterial STDs can be cured with antibiotics provided the treatment begins early enough. Note: please don't prevaricate-- get on with it for everyone's sake. Viral STDs cannot be cured, but you can manage symptoms with medications.
There's a vaccine against hepatitis B, but it/s a preventative: it will not help if you already have the disease. With regard to genital herpes, my answer won't suggest 'natural' treatment to you. If you're infected with genital herpes, the virus remains in your body for life. If may flare up several times per year, but lessen over time.
Antiviral medication helps reduce the length of each herpes outbreak and the severity. If you have outbreaks often, suppressive therapy. In suppressive means prescribed medicine for taking every day to prevent you from getting a herpes outbreak.Consider the partner who transmitted the STD to you. Is s/he the person you want to spend your life with