The northern temple uniquely has three insulated layers of flooring. The pavement on the topmost level is not marked by sacrificial fires, unlike the lower floors. Due to the different methods used in polishing the stone, scholars have theorized that the three layers of pavement illustrate three major shifts in construction at Ħaġar Qim.
Stone balls of different sizes are located alongside the walls of the northern temple and other parts of the structure. These are theorized to have been the rollers used to transport the megaliths. Excavations have revealed such rollers buried beneath the megaliths, thus contributing to a solid foundation.
Il-Misqa (English: the Watering Place), is a flat area of bare rock atop a hill nearby the temple complex. It contains seven bell-shaped reservoirs that still retain rain-water during any winter with an average rainfall. Of the seven, five wells hold water; the three wells which no longer hold water are the deepest and are joined as a single tank through subterranean channels. A monolith surmounts one of the dry holes and is theorized to have been used in drawing water from the well. An eighth well exists but is blocked up by a mature fig tree.
The water-channels cut in the surface of the rock distribute rain-water into the wells individually and the level of water in any well is kept relative to that of the immediately adjoining well.
The Northern Temple's first recess contains a round stone pillar and a rectangular slab held vertically ahead of the pillar. Resting on the slab are spherical hollows which may have served as holders in which to stand small libation jars. Jars excavated from the site are characterized by a specifically oval base, designed to stand upright when placed in the slab.
Remnants of the vertical blocks which once flanked the recess are still observable today. To the right of this chamber is another recess, containing an acoustic opening called the "oracle hole". Sound passed from the main chamber into the recess, and vice-versa. The hole has also been linked to alignments of the Summer solstice. On the right side of the chamber is a horizontal block that may have served as seating.