Diffuse pollution is hard to analyze, control and manage by its nature. Watershed models and Geographical Information Systems (GIS) are recently developed tools that aid analysis of diffuse sources of pollution. However, their applications are not always easy and straightforward. Turkey is a typical example of a mountainous country rich in rivers and streams. Due to the complex geomorphology, land-use and agricultural practices in most of the watersheds in Turkey, modelling, analyzing and managing diffuse pollution has been a challenge. The complex watershed structure forces the modellers to work with spatially high resolution data. Apart from the data, the models themselves may also cause operational problems. These issues and their probable solutions form the basis of the discussions in this paper. It acts as a guideline for modelling and analyzing diffuse pollution by emphasizing the referred problems and difficulties. Design of an Information Technology-based system tool for watershed and/or water quality modelling, which would be suitable for countries having watersheds with similar structure and problems to those of Turkey, is also outlined.