We measure ion heating following transport throughout a Y-junction surface-electrode ion trap. By carefully selecting the trap voltage update rate during adiabatic transport along a trap arm, we observe minimal heating relative to the anomalous heating background. Transport through the junction results in an induced heating between 37 and 150 quanta in the axial direction per traverse. To reliably measure heating in this range, we compare the experimental sideband envelope, including up to fourth-order sidebands, to a theoretical model. The sideband envelope method allows us to cover the intermediate heating range inaccessible to the first-order sideband and Doppler recooling methods. We conclude that quantum information processing in this ion trap will likely require sympathetic cooling in order to support high fidelity gates after junction transport. © 2014 American Physical Society.