Every scientific discipline usually focuses on problem solving which eventually plays a crucial role in order to improve research policies and planning. Evaluation of such improvement could enhance research activities. The trend of scientific research and their subjective trajectories in watershed management were analyzed by content analysis method. This study seeks shortcomings of this discipline in the two most seminal universities in Iran (University of Tehran and Tarbiat- Modares University). The results could lead policy-makers to a better scientific strategy and modify issues show universities emphasized on the state of problem which refer to second order catchment and their sub-catchments problematic issues. Erosion-sediment sub-code and regime (hydrology) sub-code are the most reputed ones in University of Tehran and Tarbiat-Modares University respectively. Overall trends more tend to hydro-technical, geomorphological and hydro-meteorological issues. It concluded that problematic issues in the universities focus on processes and their implications instead of focusing on the final outputs which were produced by models (e.g. erosion models). Socio-economic problems would contribute more in the study of human-nature relations.