The theoretical and methodological basis of the systems hierarchical spatial and temporal analysis of a drainage basin, which addresses the problems of effective management in socio-natural systems of different ranks, is considered. It is proposed to distinguish 9 orders of forms that are relevant to the analysis of drainage basins, where the first level is represented by individual aggregates and particles, and the last - by basins of large and the largest rivers. As part of the allocation of geological, historical and modern time intervals, the specificity of the implementation of processes in basins of different scales from changing states, through functioning to evolution is demonstrated. The interrelation of conditions and factors that determine the processes occurring within the drainage basins is revealed. It is shown that a specific combination of conditions and factors that determine processes in the drainage basin is associated with the hierarchy of the objects under consideration, i.e. the choice of a spatial-temporal hierarchical level is crucial for the organization of study within drainage basins. At one hierarchical level, some phenomenon can be considered as a factor, and at another - as a condition. For example, tectonic processes can be considered as an active factor in the evolution of large river basins in the geological perspective, but for small drainage basin, this is already a conservative background condition. It is shown that at the historical time the anthropogenic factor often comes to the fore, with the appearance of which in the functioning of the drainage basin, there is a need to take into account the entire complex of socio-environmental problems that can affect the sustainable state of various territories, especially in the field of water and land use. Hierarchical levels of managing subjects are identified, which are primarily responsible for effective management at the appropriate hierarchical level of the organization of the socio-natural system within the catchment area, starting from an individual to humankind as a whole.