Sea-level change has been commonly interpreted to be of eustatic origin, and many eustatic events were hypothesized for the Phanerozoic, including several 1–3 Myr long cycles in the Ordovician with magnitudes up to 100 or 200 m. However, sea-level change modeling using stratigraphic data from Northern Estonia, which was an area of slow shallow-marine (<10 m) deposition through most of the Ordovician, indicates fluctuations of no more than 20 m. In the Late Ordovician the sea level fell only twice for ∼100 m within 1 Myr during the Gondwanian glaciation. Although the sea level remained relatively stable, there were frequent 100–200 m changes of sea depths we inferred with reference to the time spans of stratigraphic units and intervals between tectonic events estimated reliably against stable durations of East Siberian chronozones (biochrons) of the Ordovician. In the absence of eustatic events, the sea-depth changes most likely resulted from rapid crustal uplift and subsidence. According to correlated well-documented Ordovician sections from East Siberia, the rate of crustal subsidence changed rapidly in different periods and in different places of the area, thus being of a regional scale. The controversy between the sea-level stability and the regional-scale variations in sea depths controlled by rates of crustal uplift and subsidence can be resolved assuming a model of variable eclogitization rates in the lower crust caused by lithospheric stress change. Our inferences undermine the traditional petroleum prediction approach implying formation of depositional traps due to rapid eustatic sea-level change.