The next stage of the planning process is to identify concerns and problems that occur in the watershed and may interfere with its functioning. The problem types that have to be considered in terms of problem identification and analysis are:

• resource use problems
• socio-economic problems
• final effects of watershed degradation
• physical problems [10].

Some of them may be evident, others have to be disclosed by more detailed investigation or consultations with the local population, or may  emerge by comparison with desired watershed conditions [13]. 

Some examples from Central Asia and Southern Africa:

• Soil erosion and common alcohol abuse are some main problems in the Thiririka catchment in Kenya.
• Soil erosion is the main problem in the Gina river catchment in southern Ethiopia.
• In the Ükök catchment in Kyrgyzstan the ain problems are overgrazing, water management problems and bad conditions of infrastructure along with lack of funds to repair the infrastructure. Thereby, the problems are interrelated. For example, the water management problem which cause a lack of feeding stuff accelerates overgrazing on the pasture land between summer and winter pastures.