A biostratigraphic analysis of the Middle Ordovician reference sections of northeastern Gorny Altai is carried out. We study complexes of pelagic graptolites and benthic trilobites from the Dapingian–Darriwilian Tuloi and Karasu Formations. For the first time for the Late Paleozoic sedimentary basins of Siberia, lithofacies and biofacies analyses of the sedimentary successions and associated paleobiota are applied to estimation of the depths of the shelf basin and the remoteness of its particular parts from the shoreline. Proposed reconstructions are based on a complex analysis of lithology and thickness of the successions and the structure of associated complexes of pelagic organisms, graptolites (including evaluation of the population density and dominating taxa). Herein we appraise the bioindicator potential of the benthic trilobite paleocommunities.