The paper presents a hybrid machine learning model for the spatial segmentation of soils by salinity using multispectral satellite data from Sentinel-2 and climate parameters of the ERA5-Land model. The proposed method aims to solve the problem of accurate soil cover segmentation under climate change and high spatial heterogeneity of data. The approach includes the sequential application of unsupervised learning algorithms (K-Means, hierarchical clustering, DBSCAN), the XGBoost model, and a multitasking neural network that performs simultaneous classification and regression. At the first stage, pseudo-labels are formed using K-Means, then a probabilistic assessment of object membership in classes and ensemble voting of clustering algorithms are carried out. The final model is trained on an extended feature space and demonstrates improved results compared to traditional approaches. Experiments on a sample of 33,624 observations (23,536—training sample, 10,088—test sample) showed an increase in the Silhouette Score value from 0.7840 to 0.8156 and a decrease in the Davies–Bouldin Score from 0.3567 to 0.3022. The classification accuracy was 99.99%, with only one error in more than 10,000 test objects. The results confirmed the proposed method’s high efficiency and applicability for remote monitoring, environmental analysis, and sustainable land management.