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The geography of Malaysia includes both the physical and the human geography of Malaysia, a Southeast Asian country made up of two major landmasses separated by water—Peninsular Malaysia to the west and East Malaysia to the east—and numerous smaller islands that surround those landmasses. Peninsular Malaysia is on the southernmost part of the Malay Peninsula, south of Thailand, north of Singapore and east of the Indonesian island of Sumatra; East Malaysia comprises most of the northern part of Borneo, and shares land borders with Brunei to the north and Indonesian Borneo to the south.

Located near the equator, Malaysia's climate is categorised as equatorial, being hot and humid throughout the year. The average rainfall is a year and the average temperature is The climates of Peninsular Malaysia and the East Malaysia differ, as the climate on the peninsula is directly affected by wind from the mainland, as opposed to the more maritime weather of East Malaysia. Malaysia is exposed to the El Niño effect, which reduces rainfall in the dry season. Climate change is likely to have a significant effect on Malaysia, increasing sea levels and rainfall, increasing flooding risks and leading to large droughts. Malaysia faces two monsoon winds seasons, the southwest monsoon from late May to September, and the northeast monsoon from October to March. The northeast monsoon brings in more rainfall compared to the southwest monsoon, originating in China and the North Pacific. The southwest monsoon originates from the deserts of Australia. March and October form transitions between the two monsoons. The wettest place in Malaysia is Kuching, Sarawak with an average rainfall of with 279 days of rain a year. The driest place in Malaysia is in Sitiawan, Perak with average rainfall of a year. It is the only country to contain land on both mainland Asia and the Malay Archipelago. Harbours are only available on the peninsula's western side, as well as Mount Tambuyukon, the third highest in the country. Mount Kinabalu, is , and is protected as it is within Kinabalu Park, a UNESCO World Heritage Site and national park. Mount Kinabalu is 55% (by margin) taller than Mount Trusmadi, Malaysia's second tallest mountain. Mountain ranges in East Malaysia tend to follow north–south or northeast–southwest paths, and the highest ranges form the border between Malaysia and Indonesia. The mountains contain many jagged limestone peaks. It houses Mount Korbu, the second highest peak in Peninsular Malaysia. These mountains are heavily forested, and mainly composed of granite. The range is the origin of some of Peninsular Malaysia's river systems. To the east of this range is the Bintang Range. It is followed by Bruit Island in Sarawak, Langkawi in Kedah, and Penang Island in Penang. The largest island shared with another country is Borneo, followed by Sebatik Island. In addition, Malaysia lies within the world's coral reef distribution. The reefs can be usually found around islands such as Sipadan Island, Swallow Reef, and Redang Island. Sipadan, an underwater mountain, is Malaysia's only oceanic island.

A recent global remote sensing analysis suggests that there were 1,713 km2 of tidal flats in Malaysia, making it the 19th ranked country in terms of how much tidal flat occurs there.

Malaysian forests can be categorised as tropical rainforests. Approximately 58.2% of Malaysia's land is covered by forest. A large amount of lowland forest is present below an altitude of due to the increase in logging since the 1960s and the increase of shifting cultivation. Over 80% of Sarawak's forests have been felled, and the logging throughout East Malaysia has polluted waterways, increased erosion, and damaged agriculture. There are over of mangroves in Malaysia. Peninsular Malaysia's west coast is home to the Myanmar Coast mangroves. The Indochina mangroves fringe Peninsular Malaysia's east coast. The Sunda Shelf mangroves line Borneo's coast.

The southernmost point of Malaysia is located in the district of Serian in Sarawak. Tanjung Piai on the southern tip of Johor is the southernmost point of the Malay Peninsula, and thus of the whole of continental Eurasia. The easternmost point is found on the tip of Dent Peninsula in Lahad Datu district in Sabah. The northernmost point is found on the northern tip of Banggi Island. The westernmost point is Perak Island, a sandstone rock which is part of Kedah state that rises at the center of the Strait of Malacca.

[[File:Singapore Johor Causeway. jpg|thumb|The 1056m These seas are marginal seas of the Indian Ocean. Off the east coast of Peninsular Malaysia is the South China Sea, which extend into the Coral Triangle. It also has an exclusive economic zone of based on nautical miles from its coastal baseline. Malaysia claims in the depth of the continental shelf or to the depth of exploration within the area below the South China Sea known as Sundaland. The territorial claim for the Strait of Malacca is shared between Malaysia and Indonesia in accordance to a treaty signed in 1970 known as the Treaty Between the Republic of Indonesia and Malaysia on Determination of boundary Lines of Territorial Waters of the two Nations at the Strait of Malacca.

thumb|right|Ayer Keroh Lake. The Bera Lake in Pahang is one of the largest lakes in Malaysia, and one of the only two natural lakes in Malaysia with Chini Lake. Pedu Lake is a long lake located from the Malaysia–Thailand border. Kenyir Lake is the largest artificial lake in Southeast Asia.

There are many systems of rivers found around Malaysia. The longest is the Rajang River in Sarawak with a length of The second longest is the Kinabatangan River in Sabah with a length of The longest river in Peninsular Malaysia is the Pahang River with a length of .

Malaysia is a megadiverse country, with a high number of species and high levels of endemism. These forests contain the Rafflesia, the world's largest flower.

thumb|right|Peninsular Malaysia Precipitation Map in December 2004 showing heavy precipitation on the east coast, causing floods there. With 189 water basins and an average rainfall of over 2,000–4,000 mm per year, Malaysia is prone to riverine, muddy floods that range from hours long flash floods, to prolonged flooding on flat, low lying land along major tributaries and main stems. 15 instances of major flooding in the region have occurred since 1926; notable floods include the 1971 floods in and around Kuala Lumpur that killed 32, affected 180,000 and prompted the launch of flood control projects in the city, 2006 and 2007 floods in Johor that resulted in 18 deaths and RM1.5 billion in damages in addition to the temporary displacement of 110,000 people, and major flooding centered around the Klang Valley in 2021–2022 that led to 54 deaths, at least RM5.3–6.5 billion in damages and left 125,490 displaced. Flooding has been a major concern in recent decades due to rapid development in river catchment areas that has led to increased surface and river runoffs, increased sediment buildup in rivers, and frequent erosion along river banks. Due to weak Coriolis forces from its close proximity to the equator, direct passages of tropical cyclones are rare for the country despite its proximity to the highly active Northwestern Pacific tropical cyclone basin. The only tropical cyclones to significantly affect Malaysia since records began were Tropical Storm Greg in 1996 and Tropical Storm Vamei in 2001; the former's passage over Sabah remains the deadliest tropical storm in the country's history, with 238 dead and 102 missing. However, tropical depressions as well as outlying storm patterns generated by passing cyclones have made landfall regularly, often leading to abnormally high rainfall and flooding, such as the tail of Typhoon Lekima striking the Malay Peninsula in August 2018, and the path of 2021's Tropical Depression 29W across central Peninsular Malaysia contributing to record precipitation and protracted flooding in the region between December 2021 and January 2022.

Malaysia is largely seismically stable with little modern history of volcanic activity, being situated entirely on the Sunda tectonic plate, between two major boundaries of the Australian Plate and Eurasian Plate in the west of Peninsular Malaysia, and the Philippine Sea Plate and Eurasian Plate at East Malaysia. Peninsular Malaysia is more accustomed to only light tremors caused by earthquakes along the Sumatran islands of Indonesia generated predominantly by the Great Sumatran fault and Sunda megathrust. However, a pair of rare earthquakes that did not originate in Sumatra were felt in much of Malaya and Singapore on 31 January 1922 and 7 February 1922. As is with Singapore, the effects of tremors are also felt more significantly on skyscrapers common in populated centres in Malaysia due to the effects of mechanical resonance. East Malaysian states, particularly Sabah, are at risk of more moderate interplate and intraplate earthquakes due to its closer proximity to active tectonic activities along the Ring of Fire, with record earthquakes in the country occurring in Sabah in 1923, 1951, 1976 and 2015 at an average of 6.0–6.5 Mw. The fringes of Sabah also lay host to a series of the country's only volcanoes at the Tawau volcanic field and off the state's coast. Prominently, Mount Bombalai last erupted during the Holocene epoch, while the last major eruption in present day Malaysia occurred during the formation of a chain of volcanic islands (prominently including Pulau Tiga) off Kimanis Bay in 1897. Interest towards tsunami risks to Malaysia has also heighten since the 2004 Indian Ocean earthquake. Although the western coast of Peninsular Malaysia was largely shielded by Sumatra from the full effects of waves generated by the earthquake, weaker deflected tsunami waves led to damage and casualties along the northwestern coast of Peninsular Malaysia, affecting coastal Perlis, Kedah, Penang and Perak. The disaster also highlights the risk of further tsunamis that may strike coasts in direct line of undersea faults, primarily around the South China Sea.

Malaysia produces petroleum and is a net exporter. Malaysia also produces liquefied natural gas as well as various other related products, most of which are found off the coasts of Terengganu, Sabah, and Sarawak. Other notable natural resources includes tin, timber, copper, iron, ore, and bauxite. Malaysia was the largest exporter of tin until the industry wide collapse in the 1980s. Tin deposits are found in areas in Selangor, Kinta valley in Perak, Pahang and Johor. There are significant deposit of gold in the Pahang towns of Raub and Kuala Lipis and also Kelantan's district of Gua Musang. Coal is mostly concentrated in the Sarawak towns of Kapit, Mukah and Silantek.

Timber can be found in the vast jungles in Malaysia, especially in East Malaysia. Malaysia's total exports of timber and other timber products amounted to MYR 23.4 billion in 2007.

Large areas of land are used as palm oil plantations, rubber plantations, and paddy fields. Malaysia is the world's largest exporter of palm oil producing 15.8 million tonnes of crude palm oil in 2007. As of 2011, the percentage arable land in Malaysia is 5.44%. Croplands consists of 17.49% while other land uses consists of 77.07%. As of 2009, irrigated land covers 3,800 km2. Total renewable water resource total 580 cubic km as of 2011.

Peninsular Malaysia is more populated than East Malaysia with 79.2% of the population living in Peninsular Malaydia. In 2002, 59% of Malaysian population lived in urban areas, while the rest live in rural areas. The largest city is Kuala Lumpur with a population of 1.89 million people in the city, and about 7 million in the metropolitan area known as Klang Valley. Other major cities include George Town, Ipoh, Johor Bahru, Kuching, and Kota Kinabalu.

thumb|A Map of Malaysia's states. Malaysia is divided into thirteen states and three Federal Territories. Eleven states and two Federal Territories are found in Peninsular Malaysia, while two states and one Federal Territory are found in East Malaysia. The states are further divided into administrative districts. In Sabah and Sarawak, they are first divided into divisions, then further divided into districts. There are separate subdivisions for electoral districts for polling purposes. International borders between Malaysia and Indonesia, Thailand, Singapore and Brunei are defined mostly by geological features such as the Perlis River and Golok River between Malaysia and Thailand; Straits of Johor between Malaysia and Singapore; and Pagalayan Canal between Malaysia and Brunei. However, borders that extends to the seas are defined by agreements such as Straits Settlement and Johore Territorial Waters Agreement of 1927 which defines Malaysia and Singapore water borders.

Malaysia's land borders are well established. The border with Thailand was established in 1909 when Siam ceded Kedah, Kelantan, Perlis and Terengganu to the British. Maritime border disputes between Brunei and Malaysia and a Bruneian claim on Limbang, Sarawak were resolved in an exchange of letters between the two countries on 16 March 2009 after 20 years of negotiations. Malaysia and Indonesia have some overlapping maritime claims, notably in the area around Sabah. An ongoing series of meetings to resolve these claims has produced 16 border agreements (to September 2010). Malaysia and Singapore also have disputes concerning some maritime borders. Malaysia is also involved in a dispute involving Vietnam, Brunei, the People's Republic of China, the Philippines, and the Republic of China (Taiwan), concerning the Spratly Islands in the South China Sea.