Western Sahara and Morocco are pretty much one country these days and you can travel all the way down to the Mauritania border. As far i am aware you don't need another permit to travel into Western Sahara but you will come across many check points. As along you have a vaild Morocco stamp in your passport you should be fine.
From Agadir you can get Supratours buses to Laayoune 11 hours and Dakhla 21 hours and I am sure CTM buses will do the same as well.
About 13km south of Agadir is Inezgane A transport hub for the south.
There is no train track in this area.
Since Western Sahara has a lot of very desolate areas and the public transportation is very poor in these area, it might be a good option to rent a car if you are interested in seeing the landscape in the country. The roads generally are pretty good (as long as you're planning to go all the way to the south or east), and a very good thing: the petrol is very cheap here!
I rented my Dacia Logan in Laayoune at a company called Massira Travel. The owner Ibrahim is a very friendly guy ( if you meet him tell him that his friend Pieter from Holland says hi ) and is very willing to help you. For a day rent they only ask 26 euro's, and there is no trouble like a compulsary fill-up of the tank after using it: as long it is about as full as you received it, it's fine.
Massira Travel can be found at 20 Avenue Mekka.
Some important tips about driving in Western Sahara:
- make sure that your gastank is always more then full enough: you don't see a lot of gasstation here!
- be prepared to see a lot of camels at the side, or even on the road. The roadsigns warning for them clearly are not for nothing.
- don't be afraid of getting lost here: first of all there are hardly any roads except for the one road from north to south, and second the roadsigns are not only in arabic, but also in latin alphabet.
- be prepared for so called "walking dunes": you'll often see sanddunes being moved by the wind, blocking a big part of the road. Big machines are always busy cleaning the roads but it's a never finished job...
- make sure your windows are closed when you cross an area like this, or you have 10 cubic metres of sand on you lap in no-time.
- you'd better keep the car-papers and your personal papers handy all the time, because you'll often need to stop at one of the many police-checkpoints to show them.
Although Laayoune is not a very big city, it is still way too big to explore the whole city on foot, unless you are a really fanatic person. For example the distance from the old Spanish (lower) town to the modern (Moroccan) city is about two kilometres, pretty steep uphill, and from there to the bazaar is about the same distance.
For these distances using the Petit Taxi (small taxi in French) is the ideal solution. The Petit Taxi is pretty cheap (3 to 5 dirhams) and it's fast. You can find them everywhere: every small red-and-white car is one, but they always have a sign "Petit Taxi" on the roof to make it extra clear.
Often the drivers don't speak English or French, but if you just mention a name of the place you want to go to, they will go there. When you have to pay, just give 3 dirhams. If they think they deserve more (up to 5 dirhams) they will make sure that they speak exactly the few French words that are necessary.
Officially (as far as I understood) there are specific places where the taxi's are allowed to stop, but according to my experiences nobody really cares about that.
If you want to go from Morocco to Western Sahara overland there are only two option you can choose from. There are no trainconnections this far south, so the only possibilities are the bus and a the shared taxi.
The cheapest option is to take a shared taxi. These depart from basically every city in the south of the country, but this is a very inconvenient option: two people are put on the passengers-seat in the front, and four people in the back. Believe me, even in the big Mercedesses that they use this is very, very tight!
The better option therefore definitely is the bus. Several companies have connection to what the Moroccans call "The Sahara Territories", but the one I used, Supratours, is one of the most comfortable and most reliable ones. In every city where Supratours goes to, they have their own office and place where they depart: don't look for them on the main "Autogares".
We took the Supratours bus to Laayoune from Agadir (Inezgane). From here it took us 12 hours to reach the destination and the costs for this were 195 dirhams (28 dollars). From Marrakesh the costs are 280 dirhams (38 dollars) and this takes 16 hours. The busses all depart in the evening and depart early the next morning.
We had our own car to cross the country, this was very convenient. En route we saw also some taxis and long distance buses.
From Laayoune the connections are rather good. There are the grand blue taxis and buses. The taxis are faster, the buses a bit more comfortable.
From Laayoune there are also flights to Dakhla, Agadir, Tan Tan and Casablanca and even the Canary Islands.
At the long long way of about 900 KM in Western Sahara from Mauritania to Tarfaya we hardly saw any traffic. Especiallay early in the morning at the southern part of the route. The first car we saw, was this truck sprinkling water in the middle of nowhere. We didn't now why.
Later in the morning we had some oncoming cars, 4 WDs and campers of travellers heading south, the ones who spent the night in El Dakhla.
40km to Dakhla you have to stop and give your papers to police cheack point. They just need to have your passport number and name to know you were there. This is for your own protectoin, cos if you somehow disapear in this huge place in western sahara they know you passed here and it will be easier to locate you...maybe...
its be talking to the police.
I know there are taxis that will take you from Dakhla to the last Police check point in Bir Gandus. They will drop you off in the border as you can see on the picture (taxis are those red mercedes). i also know that a taxi will cost around 100euros, cos you have to pay the taxi driver back to Dakhla. From the border to Dakhla (if you're coming from mauritania) can be cheaper if you make a good deal.
be careful with taxis, these region is know to have people getting kidnapped or robbed.
You can easily go with your car. be careful not to hit a landmine. after the first moroccan police cheackpoint you have 7km with bombed road and sand. as sson as you get to the first mauritanian police checkpoint you have even worse deseert tracks to get to the second police control house and "duane". from there to enter Nouadhibou you'll need a guide cos you dont know the way into the sand. even with GPS it will be hard to pass due to the large amount of landmines.
If yo ugo to KM 40 after dakhla where the police checks for peoples ID, you can get a ride from tourist going south. many people sleep in dakhla to leave in the morning to mauritanian border. I got a ride to this moroccan point and from here got another different ride. Be careful with rides from local people. there are news that some tourists, backpacking were killed while hitch hikking in western sahara towards mauritania.
remember that from dakhla to the border is almost 400km.
As you can notice this type of cars are quite useful for this area. Usualy 4WD cars drive south to Mauritania and all the way in Western Sahara, sometimes and illegaly making contact with Algeria. Tindouf stands as the bigest refugee camps in western sahara. Saharawis had to tun when Morocco took power of the country.
In all His wisdom, [insert deity here] provided man with not just one foot, but two! These can be used to get around the desert with reasonable efficiency, especially when carrying a fairly heavy rucksack, like the poor bastard in the picture next to this text!
Taxi are quite faster than buses. Some places dont even have buses. Prices here usualy are not over charged.
Lauyoune-Dakhla 150dirhams (+-15euros)