The distance between Berlin and Amsterdam is 576 kilometers or 358 miles , so walking will take far too long.
Road to Berlin:
According to a route planer on the internet the distance is about 650km. If you were in a road vehicle maintaining an average speed of 40mph (64 kmh), it should be about 7 hours to travel from Berlin to Amsterdam but hitch hiking it might take longer. Even cheaper than bus is taking a ride with someone already going to Amsterdam and sharing the petrol costs with them. This is called Mitfahrtzentrale.
Berlin Amsterdam Train:
If you were in a train Berlin Amsterdam it would take you around 6 1/2 and 9 hours to travel from Amsterdam to Berlin Germany. There are direct train from Amsterdam to Berlin and berlin amsterdam and they can be cheap if booked in advance. Trains leave about every hour during the day. On some connecting trains between Berlin and Amsterdam there are only second class seats available. If you wish to book first class accommodations for your entire journey, confirm that it is possible for your chosen route. There is only one direct InterCity train from Berlin to Amsterdam.
It operates daily, and it takes around 6 1/2 hours to arrive in Amsterdam. With the InterCity Berlin you can travel from Schiphol directly to the centre of Berlin. running every 2 hours travel time 6:30 . German rail is especially good at giving deep discounts to tickets booked at least 3 days ahead of time, even better if you book it 2 weeks in advance. If you decide to go the night before the cost is at least about 90 € each way. There is a night train, the City Night Line, from Amsterdam to Berlin, but for some reason it leaves at around 7 p.m. and arrives around 4a m. And ICE from Berlin to Amsterdam dep. At 00 and arr. At around 10 am. travel time:around 10 h savings fare are only available for round trips
The ICE Berlin Amsterdam was considerably faster than normal trains, but it is an expensive treat .
Flights Berlin Amsterdam: travel time:1h15min direct flight.
AirBerlin are no longer flying between Amsterdam and Berlin. Transavia.com, the discount Dutch airline, covers this rout . KLM do Berlin to Amsterdam flights. The direct Berlin Amsterdam train goes trough some of the most boring parts of Germany and the Netherlands. You won't be missing out on much if you fly. If you've got enough time in advance, easyjet flights to amsterdam might be still much cheaper than a train ride, but mostly cheap seats are booked out months in advance for flights to amsterdam easyjet. Both airports have good and cheap transport to the city centers, running about 30 minutes for either city.
Bus Berlin Amsterdam: travel time: about 10 hours each way
Cheapest public transport is the bus. The Eurolines has the lowest prices. Also try BVG Berlin bus. Buses run overnight so backpackers can save a night in the hostel and wake up in the other city. The bus leaves from in front of Amstel Station in Amsterdam, which is about 2 km south of Centraal Station, and easy to reach by tram or metro. Also you can try BerlinLinienBus. Discounts are available.
I personally would either fly or take the train. If you wait until the last minute your fare might be much higher, but sometimes these promo fares are even available on the day of the journey.