The Gulf of Taranto, between the Adriatic and eastern Mediterranean basins, is a gateway for water-mass exchange and transformation, yet its vertical mixing and the biogeochemical consequences remain poorly quantified. We present a full-depth transect across the Gulf entrance, sampled during the PIONEER-2023 cruise (November–December 2023), combining hydrography and velocity with dissolved oxygen, nutrients, dissolved inorganic carbon and total alkalinity. The section was occupied in a cyclonic state, with doming isopycnals in the upper 300 m lifting nutrient- and carbon-rich water. Water-mass-resolved transports describe an asymmetric but compensated exchange: a robust eastern surface inflow, a weaker, marginally resolved resident deep inflow, and an Adriatic-derived deep vein entering and leaving without a resolvable net contribution. Section-integrated budgets are indistinguishable from zero for every tracer, so the result is how exchange partitions among water masses, not a net budget. Finescale estimates reveal contrasting regimes around an oxygen minimum layer near 1000 m: double-diffusive above, internal-wave-driven below and in deeper sheared layers. Oxygen, dissolved inorganic carbon and alkalinity converge into the layer across both boundaries, preferentially from below, whereas nutrient fluxes are tracer-specific, phosphate and silicic acid differing in direction from nitrate. Because diapycnal exchange supplies oxygen from both sides, it erodes the minimum rather than sustaining it; its persistence requires consumption or advective terms a single survey cannot resolve. The Gulf thus acts as an active transformation zone rather than a passive conduit, modifying the ventilation state, nutrient content and carbonate chemistry of the water masses crossing it toward the Ionian Sea.