Fluvial channels in metamorphic core complexes are preferentially oriented parallel and perpendicular to the direction of tectonic extension. This pattern has been variably attributed to such causes as tectonic tilting during extension, channel elongation by slip along the range-bounding detachment fault, and the exploitation of extension-related joint sets during channel incision. In this paper we use field measurements, digital elevation model analyses, and numerical modeling to test hypotheses for the tectonic and structural control of fluvial channels in metamorphic core complexes, using the Catalina-Rincon core complex in southern Arizona, USA, as a type example. Field measurements and aerial photographic analyses indicate that channels of all sizes exploit steeply dipping joint sets during fluvial incision. As a consequence, channels become preferentially aligned along those joint sets. First and second Strahler-order channels preferentially exploit a joint set oriented perpendicular to the extension direction, while higher-order channels preferentially exploit a joint set oriented parallel to the extension direction. While these observations support the joint-exploitation hypothesis for structural control of drainage architecture, numerical modeling indicates that the spatial distribution of rock uplift during the initial phase of extension plays a crucial role by determining which joint set is preferentially exploited by channels of which Strahler orders. Numerical models indicate that higher-order channels exploit the joint set that is most closely aligned with the direction of initial tectonic tilting, even if that tilting is active for only a short period of time following the initiation of uplift. We conclude that the drainage architecture in the Catalina-Rincon core complex is the result of a combination of joint exploitation and tectonic tilting mechanisms. Structure also plays an important role in controlling the longitudinal profiles of channels in metamorphic core complexes. Channels in the Catalina-Rincon core complex are characterized by structurally controlled knickpoints with a wide distribution of heights and spacings. Field observations indicate that the occurrence of structurally controlled knickpoints and the resulting variability in longitudinal profile form is related to spatial variations in joint density. Numerical models that incorporate spatial variations in joint density using a stochastic bedrock erodibility coefficient are capable of reproducing the statistical properties of longitudinal profiles in the Catalina-Rincon core complex, including the power spectrum of longitudinal profiles and the frequency size distribution of structurally controlled knickpoints. The results of this study illustrate the important roles played by both jointing and the spatial distribution of rock uplift on the geomorphic evolution of metamorphic core complexes. More broadly, the study provides a recipe for how to incorporate joint-related structural controls into landscape evolution models.