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Magnetic prospecting is the most widely used method for the investigation of archaeological remains in the world. This method is often applied before and during various engineering exploration (e.g. road construction, preparing areas for various types of building) and areas of agricultural utilization. Taking into account an extremely high concentration of archaeological sites of different age at Israeli territory, prompt geophysical-archaeological assessment of areas allocated for engineering and agricultural utilization, is a necessary preliminary component of the design process. However, noise both of natural and artificial origin strongly complicates interpretation of observed magnetic anomalies. The most significant disturbing factors are oblique magnetization (magnetization vector in the Israeli territory is inclined about 45°), complex geological structure (presence of a variety of disturbing bodies) of investigated site, influence of rugged topography, as well as influence of modern iron-containing objects. The non-conventional procedures developed by the authors are intended for application in such complicated environments and include elimination of noise from various sources, selection of 'useful' anomalies against the noise background, qualitative and quantitative interpretation of anomalies and three-dimensional physical-geological modelling. Effective integration of these procedures with other interpretation methods allowed rapid localization of tens of archaeological remains and their protection from unpremeditated destruction.