Abstract The development of oil exploitation activities in Colombia carries the risk of severe environmental damages and social disruption. Since it exists a spatial high correlation between high biodiversity and hydrocarbon potentially- rich geologic formations, many of the areas targeted for oil development directly overlap with and can threat sensitive ecosystems. The last three years, the oil industry along with the Colombian Government has undertaken the project "Environmental Land-Use for Hydrocarbon Exploration and Exploitation" aimed at developing a whole set of environmental and socioeconomic parameters for the evaluation of new projects of the oil industry. These parameters or indicators will allow as well defining environmental constrains. One the main achievements of this research work is a methodology for the development a system of indicators. This paper presents the resulting preliminary indicators for the monitoring and quality assessment of tropical freshwaters. A region of Colombia, the Department of Huila (south East Colombia) was chosen as case study. Huila has rich water resources among them the Magdalena river; an important water source for domestic, agricultural and industrial use and ecologically rich waterway. It was thus clearly important to establish a methodology for assessing the impacts of oil activities on rivers. However, the existing knowledge on Huila's rivers was extremely limited and consequently, no proven methodology existed so far. A major study was therefore necessary in order to establish the physical, chemical and biological characteristics of the local river systems. The methodology developed is based on space/time relationships among the physical and chemical conditions of water bodies and their biology. Aquatic toxicity tests were performed in laboratory conditions as complementary information source on. This methodology could be equally applicable to the rest of Colombia and other tropical regions.