Strontium isotope ages of foraminifers from Early Miocene to Late Pliocene (Neogene) sequences (21.2–3.4 Ma) are reported for the first time from the Queen Charlotte Basin (QCB) in Queen Charlotte Sound, offshore British Columbia. These ages, together with a revised foraminifer biostratigraphy and log data from two offshore wells, provide a high-resolution chronostratigraphy for the southern part of the QCB. The data show thick 1717–2636 m Miocene sequences overlain by much thinner Pliocene and younger units (<240 m). Assessments of foraminifer biofacies indicate common transported neritic and shelf faunas into slope or bathyal environments where changes in basin water depths indicate significant deformation and erosion. Additional stratigraphic information for six offshore wells in Hecate Strait show the common occurrence of amorphous carbonates in the upper sections of the penetrated basin successions. Amorphous carbonates and coals are less common in the Harlequin D-86 and Osprey D-36 wells of Queen Charlotte Sound. Coals are especially common to abundant in the sedimentary sections penetrated by the Hecate Strait wells and are potential sources of seep fluids and gases. The occurrences of glassy-textured coals, zeolite-like minerals, recrystallized foraminifers, and inverted stratigraphic units in the basal parts of Miocene sub-basins indicate heating, deformation or slumping, and upward mobilization of fluids or gases after the Early Miocene. Results support syn-rift and post-rift depositional and deformational phases. Comparisons between the different geological processes and events in the Queen Charlotte and Tofino basins reveal details of the complex evolution of these Cenozoic basins, plate margins, and ridge junctions.