Magnetic susceptibility (MS) and gamma-ray spectrometry (GRS) stratigraphy were used for correlation and characterization of eight Silurian-Devonian (S-D) sections in the Prague Synclinorium (Czech Republic). They represent two different facies developments: lower subtidal to upper slope deposits and slope-to-basin-floor distal calciturbidites. Sections from relatively shallow- and deep-water sections are easy to compare and correlate separately, although the detailed relationship between these two facies is still not entirely clear and correlations between the two settings are difficult. This may be due to sharp facies transitions and presence of stratigraphic gaps. The MS and GRS stratigraphic variations combined with sedimentologic data have been also used for reconstruction of the evolution of the sedimentary environment. The beds close above the S-D boundary show noticeably enhanced MS magnitudes but weak natural gamma-ray emissions. It may correspond to an increased amount of terrigenous magnetic material occurring with short-term shallowing (sedimentological evidence). In deep-water sections the uppermost Silurian is characterized by high MS and GRS values. It corresponds to a supply of recycled sediment to the lower wedge which occurred during the late Pridoli regression phase. The basal Devonian beds correspond to gradual deepening, but the overlying sequences reflect other shallowing episodes which are expressed in increasing MS and gamma ray activity of rocks. The MS and GRS fluctuations are interpreted as a result of local subsidence of the sea bottom along synsedimentary growth-faults and/or a biotic event rather than of eustatic sea-level changes.