I'm six weeks pregnant but I have on going bacterial vaginosis. Will it harm the baby?

BV. If this is diagnosed by your doctor they should be treating this. But, most self diagnosed cases of BV are incorrect. Pregnancy produces hormones that increase swelling of the vagina and increase mucous production. This can mimic BV thus the high level of incorrect self diagnosis. Your doctor should diagnose this with a wet prep and not just by symptoms otherwise they will be misdiagnosed as well.
No. Bacterial vaginosis infections are in the vagina and don't hurt the baby. Talk with your doctor about treating it. That being said there is some indication that BV infections later in pregnancy are associated with a higher incidence of premature labor. Rarely BV might be associated with an infection in the uterus also later in pregnancy.