The village lay on rolling terrain on the southern coastal plain, on a bend in a wadi. Secondary roads linked it to the Gaza–Bir al-Sabi' highway and to adjacent villages as well. During the Mamluk period (1250–1517) the lands and surplus agricultural produce of the village were dedicated as a waqf (pious Islamic foundation) for the maintenance of the Dome of the Rock, in Jerusalem, and for maintaining another mosque in Gaza. In 1596, al-Muharraqa was a village in the nahiya of Gaza (liwa' of Gaza), with a population of 457. It paid taxes on a number of crops, including wheat and barley, as well as on other types of produce, such as goats and beehives. It seems that the sixteenth century village was abandoned some time during the seventeenth or eighteenth centuries, since it is not mentioned by travelers during these years. It was very likely reoccupied in the late 1870s.
The overall layout of the village was rectangular, and it continued to expand in modem times in a rectangular pattern along the roads leading to the highway and the village of Kawfakha. The villagers were Muslim, and their houses were made of mud bricks. The village had a mosque and a school that was opened in 1945; sixty students were enrolled in the mid-1940s. The mosque, school, and a number of small shops constituted the village's nucleus. Water for household use was mainly obtained from a deep (90 m), slightly salty well, but was supplemented with rainwater that collected in some shallow domestic wells.
Rainfed agriculture was the community's main source of livelihood, with grain, especially barley, being the chief crop. In the final years of the Mandate the villagers also planted fig and almond trees and cultivated grapes. In 1944/45 a total of 12 dunums was irrigated or used for orchards, and 4,622 dunums (on public land) was allotted to cereals. The archaeological remains found in al-Muharraqa included mosaic floors, cisterns, and marble and pottery fragments. While the village is not mentioned in Byzantine sources there is evidence that it was in fact occupied during this period.
The village was raided by the Palmach's Negev Brigade on 27–28 May 1948, at the same time as Kawfakha. The New York Times reported that it was captured by 29 May. Israeli historian Benny Morris relates that the inhabitants of the village were driven out at this time, but the village was apparently not thoroughly destroyed and depopulated until 16 August. At that time, Israeli forces were officially observing the second truce. However, Morris writes that they proceeded to mine and destroy the village for reasons described as 'military.'
The settlement of Yakhini, established in 1950, is on village lands, north of the site.
According to Morris, the Israeli settlement of Tequma ('T'kumah' in Morris) was established on the lands of al-Muharraqa in 1949. Strictly speaking, however, this settlement is on lands that formally belonged to the city of Gaza, even though it is only 2 km west of the village site.
The site is overgrown with thorny plants and short grasses and surrounded by eucalyptus trees. It is marked by piles of rubble from buildings, including the village diwan (a meeting and guest house). There are also the remnants of a mill and a well. The cemetery, overgrown with wild vegetation, still exists, in a dilapidated condition, and the fallen superstructure of one of the tombs is visible. The lands in the vicinity are cultivated by Israeli farmers.