Getting around Benin is straightforward if you are patient and flexible. The main north-south highway from Cotonou to Parakou and beyond to the Niger border is paved and in reasonable condition. The coastal road linking Cotonou to Grand Popo and the Togo border to the west, and to Porto Novo and the Nigeria border to the east, is also decent.
Bush taxis and minibuses are the main form of public transport. They run between all major towns and leave when full -- which can mean waiting an hour or more. Cotonou to Abomey takes about two hours, Cotonou to Parakou about six. Fares are low. Conditions range from acceptable to seriously overcrowded.
Zemidjans (motorcycle taxis) are everywhere and are the standard way to get around within cities and towns. Agree on a price before you get on. They are cheap, fast, and slightly terrifying -- helmets are theoretically required but rarely provided. In Cotonou, they are the only practical way to navigate the traffic.
Car rental with driver is worth considering if you plan to cover a lot of ground, especially in the north where public transport becomes sparse. Agencies in Cotonou can arrange this, and a driver solves both the navigation and the language problem. Driving yourself is possible but not recommended unless you are experienced with West African roads and traffic.
There is no rail service for passengers. Benin once had a railway line from Cotonou to Parakou, but it has not operated reliably in years.
For Ganvie, you take a pirogue (motorized canoe) from the town of Abomey-Calavi, about 15 km north of Cotonou. Boats can be hired at the lakeside for a round trip.
Road quality drops significantly on secondary routes, especially in the north and during the rainy season. If you are heading to the Somba villages or Pendjari National Park, allow extra time and ideally travel in a 4x4.