Silica diagenesis leads to dramatic petrophysical variations in the host sediment across the depth of an opal-A to opal-CT transition zone. Predicting the present-day diagenetic status of opal-A to opal-CT transition zones, i.e., active versus fossilized fronts, is essential to constraining the drivers that control abrupt changes in the physical state of sediment. This study assesses whether there are modern signatures of ongoing silica diagenesis in the sediment pore water, and demonstrates the potential for pore-water-chemistry profiles for distinguishing between active opal-CT precipitation and fossil transition zones. Pore-water chemistry, mineralogy, and thermodynamic analyses of the Ocean Drilling Program Wells 794 and 795 indicate that solubility equilibrium has been reached with respect to opal-CT in the transition zones captured by the Neogene biosilica in the Sea of Japan. Even though silica dissolution might be triggering a reverse-weathering process, the equilibrium reached with respect to diagenetic opal strongly suggests that the silica drop across the transition zones is mainly influenced by active opal-A to opal-CT transformation. Owing to abrupt petrophysical variations associated with opal-CT formation, other interstitial profiles—major ions and primary parameters—have been influenced by silica diagenesis. The extremely low silica diffusion fluxes in the sediment, the low permeability of host sediment, and the occurrence of considerable pore-water loss at the depth of the transition zone all support this conclusion that the dissolved species have not been diffused in the sediment at rates comparable to those by pore-water advection. Advection and diffusion, however, appear to have ceased recently because they have failed to smooth the signature of ongoing silica diagenesis. The porosity drop during opal-A to opal-CT diagenesis at Sites 794 and 795 is principally attributed to chemically induced anomalous compaction, causing the sediment framework to lose its strength under fragmentation and extensive opal-A dissolution.