The origin of unusual magnetic initially sedimentary rocks of the Mottled Zone (MZ) in Israel and Jordan remained enigmatic for several decades until integrated characterization of the MZ area was achieved by ground magnetic measurements and geologic observations along representative profiles in parallel with reprocessing and reinterpretation of available aeromagnetic and gravity data. Micromagnetic profiling was combined with gamma-radioactivity measurements, and representative samples were selected to determine rock physical properties. Results of field measurements, reduction and transformation of geophysical fields, anomaly inversion, and forward modeling accompanied by geologic analysis suggest that two types of magnetic anomalies and local gravity minima in the MZ areas are related to the same event, i.e., deep hydrocarbon flow associated with fossil mud volcanism. Physicochemical interaction of deep hydrocarbon flow and surrounding sedimentary rocks caused widespread weak magnetization and corresponding aeromagnetic anomalies. Other scattered heterogeneous magnetization and linked ground magnetic anomalies are common for surface/near-surface local sources and are caused by the burning of combustible gases ejected by mud volcanoes; such origin of the magnetization is confirmed by magnetic measurements of burned rocks in mud volcano areas of the Caucasus. Increased radioactivity of the lower part of the MZ likely indicates mud ejection from a deep uranium-enriched source. Locations of MZ outcrops commonly coincide with residual gravity minima, showing zones of disintegration and possible hydrocarbon accumulations. Seismic prospecting data support the existence of disintegration zones at depth. Results show the need for additional geophysical studies and a potential for revealing hydrocarbon accumulations in the MZ areas, particularly at the Halamish, Nevatim, Ma'ale Adumim, and Nabi Musa sites.