It seems you are on a motorbike. I have done the trip three times in a Landcruiser taking between five and eight bikes along.
If you leave Segou the first 100km or so is tar to Makala, then piste to Timbuktu. WE took the route Makala, Nampala, Lere, Niafounke (meet the river here), Goundam, Timbuktu. About 700km altogether. The piste is rough in places. None of the bikers had major problems but I was carrying all their baggage. There are some patches with thorn trees which caused some punctures but these are avoidable. The biggest problem for bikes is that the piste tends to be rutted in places -especially near the river- the sand blows into these ruts over time and it can be dificult to keep control, but taking it easy should avoid this.
Food available in some shops along the way, water (impure?) in all the above named villages. Fuel (petrol) in Segou, Markala and Timbuktu, maybe in Nampala. I would not bet on it being in Timbuktu though. Consumption for Segou-Timbuktu was Suzi DR600 62l; DR800 Big 67l; XT600 (1987)57l; KTM 620 73l; Kawa KMX 400 54l. All of this included messing around in the dunes for a day or two but they had no baggage. A 60 series Landcruiser carrying 900kg of baggage needed 120l without messing around in the dunes.
Timbuktu-Gourma-Doro (main Gao-Mopti road). Not easy, lots of ruts to Gourma, cross the river on a ferry and a good amount of dunes to Doro but very beautiful. Food and water in Gourma and Doro, no petrol along the route.
Timbuktu-Gao; dont know never done it.
Ferry; On bikes you can take a pirogue or pinasse (big open canoe type boats) from any two points along the river, but take care about loading the bikes, they probably wouldnt give too much of a shit if it falls overboard, but the river isnt that deep anyway!! Prices I dont know but the pirogue is usually at least 33% cheaper than the big boat. As the main Bamako-Mopti-Gao road is in good condition I cant really recommend the boat for any long journey. They also have Sweet F*** All booze on it (from what I heard).
Dont ask me about security, I know there are banditos in the area, some people have been killed so make your own mind up.
Along with this the further you move away from Markala the less traffic there is ie virtually none. If you dont have a 4x4 and are a few bikers travelling together then think about renting a 4x4 to take all your stuff, it could make the difference between a hard slog and a great laugh in the desert. A Landcruiser or Hilux from Segou with driver costs about 40-50,000 per day not including fuel.