The islands of the Maltese archipelago lie in the central Mediterranean Sea, some 90 km (~ 50 mi) south of Sicily. With just over 316 km² in land area, Malta is one of the world’s smallest states, and also one of the most densely populated.

 Numerous bays along the coastline of the islands provide good harbours. The landscape consists of low hills with terraced fields. The highest point in Malta is at 253m. There are no permanent rivers but only occasional torrents at times of heavy rainfall.

Dating to the Oligo-Miocene era of the Tertiary period (ca. 30 to 23 million years ago), the archipelago is entirely composed of sedimentary rock. Four distinct rock layers constitute the basic geology.  

When undisturbed by land faulting, the horizontal stratification Lower Coralline Limestone, a hard and well-jointed rock-type, is commonly exposed in coastal cliff-regions alongside the western coast of Malta, but rarely occurs inland.

Globigerina Limestone outcrops cover large areas of land in central and SE Malta and western Gozo, and constitutes the islands’ main building resource. Its thickness varies considerably, from ~200m in SE Malta, to the thinnest layer (22m) recorded on Gozo.

Overlying this limestone is a Blue Clay deposit, which may reach a thickness of 70m. It is due to the presence of this clay deposit that a perched aquifer exists. An important and easily accessible resource, recognised since antiquity, numerous water galleries are dug into Upper Coralline or Greensand strata (see below) in order to extract water stored above this impermeable clay deposit. Clay was also used for local pottery production. It is only in the NW Malta that substantial clay deposits are available.

Upper Coralline Limestone is the youngest rock formation, and is carboniferous in nature. Four subdivisions of this rock stratum have been identified. Of particular importance to the study of the local cave-dwelling phenomenon is the Mtarfa Member, in which the majority of the caves are located. The thickness of this stratum varies from 12m to 16m and is composed of massive to thickly bedded carbonate mudstones and wackstones. The carbonates become white and chalky and, due to their friable nature, can be easily quarried. The Għajn Melel Member forms the lowermost Upper Coralline Limestone subdivision.

Today’s Maltese climate is typically Mediterranean and is characterised by hot dry summers and warm wet winters, while the average annual temperature ranges from 14.9°C to 22.3°C and the average annual precipitation is 568 mm. Insufficient and erratic rainfall creates regular drought conditions and makes water a limited resource. The occurrence of climate shifts in the Mediterranean region since antiquity is still the subject of controversy and debate. Geological and historical evidence suggests that climatic conditions in Roman times were not appreciably different from those of the present day but were subject to temporary and minor, wetter and colder interludes.

Rock strata such as Upper Coralline Limestone allow rainwater to percolate freely through them until its meets impermeable strata such as Blue Clay, or thick marly deposits embedded within the Globigerina Limestone layer. In the latter case, water percolation is slow and much of it is lost as runoff surface water. These underground water deposits, present within the Upper Coralline and Lower Coralline layers, provide Malta with its most abundant and reliable water resource: the ‘perched aquifer’ (= water deposits under Upper Coralline outcrops); and the ‘mean sea level aquifer’ (= water deposits within the Globigerina Limestone and Lower Coralline outcrops).

Only an estimated 16–25% of the annual rainfall manages to percolate through the rock fissures and is eventually stored in either of the water tables. Today deep boreholes pump water from both aquifers. Upon its discovery around 130 years ago, the mean sea level water table became, until a couple of decades ago, the island’s main source of water supply, and since then full exploitation of the perched aquifer’s potential for potable purposes effectively ceased. 

The mean-sea-level aquifer is a renewable water source found in most areas of Malta and covers an area of 216.6 km². Its first commercial use dates back to 1887 when the first mean-sea-level pumping station at Wied il-Kbir in the territory of Qormi was commissioned. Current extraction is rampant but accurate extraction data is not available.  It is probable that current extraction levels exceed the mean-sea-level aquifer’s recharge rate. The entity currently in charge of water distribution in Malta is the Water Services Corporation. It operates four RO desalination plants with a total nominal capacity of 100,000 m³ per day.