The Eastern Mediterranean continental slope offshore Israel became a focus of exploration for, and production of, natural gas in recent years. The 2010–2011 Nautilus ROV expedition performed detailed video recordings and sampling in two areas offshore Israel: the Palmachim disturbance, southwest of Tel Aviv, and an area offshore Acre, north of Haifa. An analytical programme regarding the carbonate structures was carried out, examining the overall mineralogy, stable C and O isotopes, and Ca, Mg, and Mn concentrations. This provided information on their composition and as a result, an indication of the carbon sources and temperature of formation. The major authigenic minerals identified comprised magnesian calcite, dolomite, aragonite, and kutnohorite. The detrital minerals included quartz, clays, feldspars, and rare augite and enstatite, likely transported from the Nile estuary. The carbon isotope composition of aliquots taken from nineteen samples from these areas have an overall δ13C range from −62.0 to −0.1‰PDB, indicating a range of microbial/biogenic and thermogenic methane contributions. The range of δ18O from 2.7 to 7.0‰PDB reflects the range of temperatures of formation. The δ18O characteristics differ among areas. In general, high values; δ18O >5‰PDB are recorded from area N2 of the Palmachim disturbance, indicating low temperature of formation. Low values of δ18O (<5‰PDB) were measured from areas W2 and W3 of the Palmachim disturbance, together with samples from area N2 of the Palmachim disturbance, and samples from areas A1 and A2 offshore Acre indicate high temperature origin. Samples from an inactive chimney from area N2 range from pure dolomite to pure magnesian calcite. This trend is linked to δ13C increase from −39.9 to −0.1‰(PDB), and δ18O decrease from 6.2 to 4.7‰(PDB). These values indicate a decrease in the methane-derived carbon contribution and an increase in temperature. Kutnohorite, Ca(Mn2+, Mg, Fe 2+)(CO3)2 is a major component in samples from Acre, and less so in the Palmachim disturbance. An exploratory investigation of the relationship between Mn/Ca, δ18O and δ13C revealed that samples having Mn/Ca < 0.1(wt./wt.) have δ13C<−50‰PDB indicating a microbial methane source, while samples with Mn/Ca > 0.1 have δ13C between −35 and −22‰PDB suggesting a thermogenic origin. These results suggest that the mineralogical, isotopic δ13, δ18O, and chemical (Mn/Ca indicative of kutnohorite) characteristics of surficial carbonate structures can indicate and distinguish between deep and shallow methane sources in the Eastern Mediterranean.