Saturated hydraulic conductivity (Ks) is controlled by a suite of soil processes operating at various scales. Little is known about the spatial variability of Ks along a slope and how it is changed through the planting operation process and the specific scales at which the controlling factors function. The objective was to characterize the scale-dependent relationships between Ks and various soil processes and thereby to identify the primary controlling factors of Ks. On a typical slope transect of 900 m in the black soil region of Northeast China, Ks and six soil properties of bulk density (BD), wet-aggregate stability (WAS), surface roughness (SR), soil organic carbon content, sand and clay contents were investigated in an interval of 20 m before and after mechanical sowing in the spring. Statistical correlation analysis, its combination with noise-assisted multivariate empirical mode decomposition (NA-MEMD) and wavelet coherence were employed to examine the interactions between Ks and each factor at different spatial scales. The BD was admittedly the dominant factor controlling Ks, followed by WAS and SR before and after sowing, respectively. The statistical correlation analysis only detected the significant interactions between Ks and BD, whereas the essential influence of WAS and SR were revealed upon frequency component decompositions by NA-MEMD and biwavelet coherency. Applying multiple wavelet coherence, BD was believed adequate in explaining Ks variability before sowing, whereas the combination of BD and SR was suggested in the case after sowing. These findings hold important implications for precise Ks estimations in the black soil region of Northeast China as well as other similar regions, and also demonstrate the effectiveness of NA-MEMD and wavelet coherence in untangling complex scale-dependent relationships among soil processes.