Quantification of pg/L levels (i.e., 0.6 mBq/L) of radioactive technetium-99 (99Tc) was achieved within 15 min in the presence of isobaric and polyatomic interference sources such as ruthenium-99 (99Ru) and molybdenum hydride (98Mo1H) at 3–11 orders of magnitude higher concentrations. Online solid-phase extraction–inductively coupled plasma–quadrupole mass spectrometry (ICP–QMS) with oxygen (O2) dynamic reaction cell (online SPE–ICP–MS–DRC) was shown to be a thorough automatic analytical system, circumventing the need for human handling. At three stepwise separations (SPE–DRC–Q mass filters), we showed that interference materials allowed the coexistence of abundance ratios of 1.5 × 10–13 and 1.1 × 10–5 for 99Tc/Mo and 99Tc/Ru, respectively. A classical mathematical correction using the natural isotope ratio of 99Ru/102Ru was used to calculate the residues of 99Ru. Using this optimized system, a detection limit (DL; 3σ) of 99Tc was 9.3 pg/L (= 5.9 mBq/L) for a 50 mL injection and sequential measurements were undertaken at a cycle of 24 min/sample. For the measurement of a lower concentration of 99Tc, an AG1-X8 anion-exchange column was used to study 20 L of seawater. Its DL was approximately 1000 times greater than that of previous methods (70.0 fg/L). Thus, this method withstands coexistences of 5.8 × 10–18 and 3.5 × 10–9 for 99Tc/Mo and 99Tc/Ru, respectively. Spike and recovery tests were conducted for environmental samples; the resulting values showed good agreement with the spike applied.