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The deterioration of Mayan sites occurs through both environmental and human means and is vital to understanding Mayan Civilizations. To understand how a particular site has deteriorated over time, an archeologist may look at a number of different factors depending on the known history and geographic location. Deterioration from looting and defacement can destroy vital information about a particular site yet, the natural forces of reforestation and erosion can equally degrade archeological sites.

= Causes =

Biodegradation
Limestone is the dominant material used in Mayan architecture, in large part due to its abundance in the region. Limestone however is a relatively soft stone and can deteriorate easily. Microorganisms living on the surface of the limestone create acids that slowly eat away at the stone, creating cracks, fissures and weak points on the stone. over a long enough time, the biofilms these microorganisms create can completely erode the stone. Mayan archeological sites are spread over a number of different environments that directly effect the condition and amount of information gathered from a site. Many of the Mayan archeological sites are especially prone to the effects of the Yucatans climate, lending to biodegradation due to a warm, humid and generally equatorial climate. However, of the Mayan sites discovered, those in the Guatemalan highlands in and around the Chiapas region enjoy more alpine and subalpine habitats, with elevations 2600-2800 meters above sea levels. As a result these Highland sites are less likely to experience biodegradation to the degree that hotter, wetter subtropical climates of the lowland sites do.

Rising sea levels
Rising sea levels have submerged a number of different Mayan Archeological sites such as Stingray Lagoon and Wild Cane Cay, in Belize. At the site of Stingray Lagoon, artifacts relating to the production of salt were found underwater including pottery used to boil down brine, a process known as sal cocida. At Wild Cane Cay, evidence suggests the site was used as a trading post with deposits dating from both the Classic and  Post Classic periods, submerged about a meter underwater. Similarly submerged remains extend about a meter to a meter and a half in depth at other sites in the area, known as the Port Honduras, suggesting a dramatically different environment at the time of occupation. It is also important to note that the speed at which a site becomes inundated by water can have large effects on the condition of the remains. A gradual rise in water levels could partially expose the remains to erosion through the wave force, and a fast rise in water levels could leave a completely submerged site relatively undamaged. As a result the condition of underwater remains and the amount of decay can infer insights into the location and the cause of its abandonment, however every site is different what can be true of one archeological site may not be true for another.

Intentional destruction
The intentional destruction of Mayan antiquities has left a large gap in the understanding of Mayan perspectives. Nearly all Mayan texts, known as codices, were destroyed by spanish conquistadors during the time of colonial expansion in Mesoamerica. Beginning in the mid fifteenth century laymen such as Fray Diego de Landa conducted inquisitions, destroying Mayan codices, believing them to be idolatrous, as well as torturing and killing local populations believing they were practicing human sacrifices. Ironically, some of the only surviving interpretations of codices come from De Landa's own personal notes and from his Relacion de las cosas de Yucatan. In other cases building materials used for the construction of colonial era buildings such as churches, were taken directly from Mayan remains, these buildings in turn were reused in later constructions. Degradation of Mayan sites due to human effects has had a resurgence as Tourism grows in popularity. In some cases out right defacement and Graffiti has permanently altered Archeological remains. In other cases it is a slow degradation due to overuse as thousands of tourists visit Mayan sites every year.