Honeycomb weathering is a common surface phenomenon affecting a variety of rocks in a range of environments. The processes involve the progressive of closely spaced cavities which are generally small with an average width few millimeters to several centimeters in diameter. Honeycomb weathering, also known as fretting, cavernous weathering, alveoli/alveolar weathering, stone lattice, stone lace or miniature tafoni weathering. Incipient honeycomb weathering in a homogeneous limestone has been experimentally reproduced by wind exposure and salt crystallization. It is a type of salt weathering common on coastal and semi-arid limestone. Honeycomb weathering occurs in many populated region and must have been noted in archaeological sites at Leptis Magna (Libya). Leptis Magna is a World Heritage site on the Mediterranean coast of North Africa in the Tripolitania region of Libya. In order to create an appropriated conservation concept, it was necessary to investigate the damage processes. For this purpose, X-ray powder diffraction (XRD), optical and scanning electron microscope (SEM) attached with EDX, Stereo microscope, polarizing microscopes (PM) were used. Bio-deterioration problems in the site were analyzed taking into account their impact on the substrate and their relationship with environmental factors. Chemical analysis and field observations indicated that honeycomb weathering in coastal exposures of limestone at archaeological sites of the Leptis Magna results from evaporation of salt water deposited by wave splash from Mediterranean Sea. Microscopic examination of weathered samples show that erosion results from disaggregation of minerals grains rather than from chemical decomposition. Thin walls separating adjacent cavities seem to be due to protective effects of organic coatings produced by microscopic algae inhabiting the rock surface.