The wall was not separating East Berlin from West Berlin. It was separating West Berlin from East Germany.

Here is an interactive map of where the Berlin Wall was.

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As the night of August 12, 1961 came to a close, at Midnight, Soviet soldiers broke the border between East and West Berlin. They used barbed wire, broken roads (that they broke), and tank traps to stop people from going across the border. They also severed major crossings between West Berlin and East Germany. By morning of August 13, when people began their daily commute between East and West Berlin, people began to understand what was happening. During the time the wall went up, soldiers protected the wall from East Berliners attempting to defect.

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Over time, the wall got more and more sophisticated. A "No-Man's Land" was created by making a 100 meter "No-Man's Land" by razing houses and buildings, and this area became known as the Death Strip. Mines were laid. Tank traps were laid. Guards were stationed (first with orders to shoot on sight with orders to shoot to kill coming later). The wall got bigger. Train stations were shut down. Eventually, the only way from West Berlin to East Germany was through heavily guarded checkpoints, such as Checkpoint Charlie, or direct access from West Germany to West Berlin via train, but they were heavily guarded. At its peak, the wall was 155 km long and it was surrounding West Berlin.

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When countries like Estonia became independent, East Berliners could (and did) travel to these independent countries, and then flew into West Berlin. These loopholes were shut down as quickly as possible.

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East Berliners tried to get into West Berlin in any way they could. With major checkpoints shut down, other ways were created. Tunnels, swimming, and well timed runs climbing the wall while patrols were gone were attempted. They were all countered. The Death Strip made tunnels be at least 110 meters long. Soldiers would shoot swimmers and runners. Runners had to climb a four meter tall wall with a smooth pipe on top. If someone was shot while running across the Death Strip, they were left to bleed out.

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They tried to get around the wall, but the wall encircled West Berlin. It did not separate West Berlin from East Berlin. It seperated West Berlin from East Germany.