Buses run from Gao to Mopti and Bamako. The fare to Bamako is 15.000 CFA, to Mopti about half that. Another option is taking the passenger boats on the Niger river, they stop by Timbuktu which makes for a very nice excursion.

For onward travel to Niamey in Niger you cannot take a boat, since the river is not navigable all the way. There are buses three times a week, try the SNTN office. The bus stops overnight at the border and arrive the following day. The fare is about 8000 CFA. Take water with you.