There are several transportation options from Hanoi to Halong.

Car transportation (interprovincial bus, private car...)
Car transportations such as interprovincial buses, tourists buses, private cars, and motorbike is the most popular option that tourists choose to travel from Hanoi to Halong. The reason that makes most tourists choose this type of transportation is that the road and bridge tolls are quite cheap. Also, about 3 hours and a half sitting in a car with air-conditioning and cushioned seats seems comfortable and relaxing to many tourists.
There are various choices for tourists when it comes to car transportation. Usually for a large group of tourists who travel in a tour, the travel agencies will prepare a bus for them so they don’t have to worry about it. For individual or small group of tourists who travel by themselves, Vietnamese interprovincial buses could be an ideal choice. However, the tourists should carefully secure their property (particularly small items such as cellphones, purse or jewelry...), purchase tickets only at the bus station, and never get in any buses that pick up on the road. In the worst case, taxi is also a choice, but it will cost a little bit extra.
Train transportation
For tourists who adore the joy of observing landscape while traveling by train, train travel is a great option. The train starts at Yen Vien Station (Hanoi) at 5:15am, and it takes about 7 hours to reach Halong City. The magnificent view of endless rice field, forest, and ocean on the road will remain in passenger’s memory as a unique experience. However, the train might be a nightmare for any clean freak. It is not too dirty, but it neither spotless.
Helicopter transportation
This is new a service provided by Northern Services Flight Company since 2008. It takes only 45 minutes to get to Halong City with $350-420USD for a one way ticket and $550USD for a round trip ticket. Beside regular transportation, this company also provides see-sighting services for tourists. It is quite fascinating having a panoramic sight of Halong Bay from above.
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