The Wooley Creek batholith, Slinkard pluton, and associated hypabyssal intrusive rocks constitute a large-volume, Middle Jurassic (∼162 Ma) magmatic system in the north-central Klamath Mountains of California. Tilting and erosion subsequent to Nevadan thrusting exposed a structural section at least 9 km thick. The system is heterogeneous with reference to initial 87Sr/86Sr (Sri) and δ18O, including mafic selvages and mafic dikes that intrude the Wooley Creek batholith and its roof rocks. Structurally lower parts of the plutonic system have average Sri = 0.7048 and δ18O = 8.2‰. Structurally higher parts have average Sri = 0.7044 and a range of δ18O that is positively correlated with SiO2 content. Two-mica granite in the Slinkard pluton has Sri = 0.7046, δ18O - 12‰, and is compositionally and mineralogically distinct from the rest of the system. Roof-zone dikes above the Wooley Creek batholith show a range of δ18O and Sri that was caused by varying degrees of equilibration with host metamorphic rocks. Host rocks of the structurally higher part of the system have a range of Sri and high δ18O, whereas metasedimentary xenoliths in structurally lower parts of the system have high Sri and δ18O from 9.0‰ to 10.9‰. Field relations indicate that the system grew by periodic injection of mafic and intermediate magmas rather than by two pulses of isotopically distinct magmas. Field, trace-element, and isotopic data can be explained by combined in situ fractional crystallization, magma mixing, and assimilation. Assimilation of 87Sr-rich wall rocks at lower levels and of 87Sr-poor, 18O-rich wall rocks at higher levels resulted in the heterogeneity observed in the system. Inclusion of our data set with other isotopic data for Klamath granitoids shows that pre-Nevadan plutons have slightly higher Sri than post-Nevadan plutons, despite the apparent increase in crustal complexity and radiogenic nature of the Klamath crust during the Nevadan orogeny.