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Despite progresses in representing different processes, hydrological models remain uncertain. Their uncertainty stems from input and calibration data, model structure, and parameters. In characterizing these sources, their causes, interactions and different uncertainty analysis (UA) methods are reviewed. The commonly used UA methods are categorized into six broad classes: (i) Monte Carlo analysis, (ii) Bayesian statistics, (iii) multi-objective analysis, (iv) least-squares-based inverse modeling, (v) response-surface-based techniques, and (vi) multi-modeling analysis. For each source of uncertainty, the status-quo and applications of these methods are critiqued in gauged catchments where UA is common and in ungauged catchments where both UA and its review are lacking. Compared to parameter uncertainty, UA application for structural uncertainty is limited while input and calibration data uncertainties are mostly unaccounted. Further research is needed to improve the computational efficiency of UA, disentangle and propagate the different sources of uncertainty, improve UA applications to environmental changes and coupled human–natural-hydrologic systems, and ease UA’s applications for practitioners.