The boundary is formed by straight lines between maritime geographical coordinates running along or near the deepest channel of the Straits of Johor.

There are also international ferry and bumboat services between Pengerang at the southeastern tip of Johor, Malaysia and Changi at the eastern end of Singapore.

A large extent of the Malaysia–Singapore border is defined by the Agreement between the Government of Malaysia and the Government of the Republic of Singapore to delimit precisely the territorial waters boundary in accordance with the Straits Settlement and Johore Territorial Waters Agreement 1927 as being straight lines joining a series of 72 geographical coordinates roughly running about 50 nautical miles (93 km) along the deepest channel (thalweg) between the western and eastern entrances of the Straits of Johor.

The 1995 agreement also states that the border will be final and, therefore, not be influenced by any variation of the depth or alignment of the deepest channel of the Straits of Johor.

This is important considering frequent reclamation activities by both Malaysia and Singapore in the Straits of Johor which could alter the depth of the waterway.

In 1979, Malaysia published a map[5] unilaterally defining its territorial waters and continental shelf, "picking up" from where the 1927 agreement left off as far as the Malaysia–Singapore border is concerned.

In 2018, Malaysia published in its Federal Government Gazette changes to the Johor Bahru port limits that extrapolated from the 1995 territorial waters agreement.

The unilateral move drew a strong protest from Singapore's Maritime and Port Authority (MPA) who asked the mariners to ignore that notice.

It then continues in a general easterly direction to meet the southern terminus of the Indonesia-Malaysia border as defined by their continental shelf boundary agreement of 1969.

[9] Further complications could arise by the awarding of Middle Rocks, which lies 0.6 nautical miles (1.5 km) south of Pedra Branca (i.e. away from the Johor coast), to Malaysia.

On 16 March 2020, both the Malaysian and Singaporean governments announced that both Malaysia and Singapore would implement border restrictions in response to the COVID-19 pandemic.

[12] Two years after the full closure, the Causeway and Second Link were finally reopened at both sides to all forms of private transportation.

[15] Malaysian and Singaporean governments have been involved in a range of disputes and disagreements which had tested the bilateral relations between the two countries.

Pedra Branca is a rock formation located at the eastern entrance to the Singapore Straits to the southeast of the southeastern tip of Johor, Malaysia.

Together with two other marine features called Middle Rocks and South Ledge, they were subject to a sovereignty dispute between Malaysia and Singapore.

The decision settles a long-standing barrier to the negotiation process for the determination of the maritime boundary between the two countries and both Malaysia and Singapore said immediately after the ICJ decision that a joint technical committee would be set up to determine the maritime border in the waters around Pedra Branca.

[16] This dispute resulted from Singapore's reclaiming of land in two areas, namely in the southwestern end of the island called the Tuas development, and in the waters adjacent to Pulau Tekong in the Straits of Johor.

[18] In 2003, Malaysia submitted a case to the International Tribunal for the Law of the Sea and requested for provisional measures against Singapore's reclamation works, including that concerning Point 20.

[21] Singapore's Agent Professor Tommy Koh said, "The happy news, of course, is that the two delegations were able to agree on the appropriate way in which these recommendations would be implemented", which allowed both countries to come to an amicable solution which resulted in the termination of the arbitration proceedings.

Since 1 July 2011, WTCP was the southern terminus of the KTM rail network and the checkpoint houses both Malaysian and Singaporean border control facilities.

In 1998, Singapore opened the Woodlands Train Checkpoint and moved its immigration post there, the official reason being improving border security.