The availability of computer packages for hydraulic modeling and water quality in rivers in quite wide. However, with the best knowledge of the research team, the available conventional packages have been developed with simplifications and assumptions for conditions that drastically differ from morphology and hydraulic present in the Andean area, especially in rivers of high slopes. The predictive capacity of the most commonly used models is, therefore, questionable to apply their results in analysis and projections in the high Andean morphological reality; And, much more questionable to serve as a platform for water quality modeling. The development of new flow transit models in high slopes is crucial to expand knowledge of the Andean hydrological system, for infrastructure design, the analysis of future scenarios; And obviously to correctly predict the transit and transformation of pollutants. The incorporation of quality models on a rigorous hydrodynamic solution allows in the integrated model resulting the prediction of water quality scenarios to natural and anthropic actions in the river. Therefore, the mathematical and numerical development of a hydrodynamic model that considers the forgotten morphological regional factors in conventional models, which involve greater complexity in the resolution, but will mean to provide scientists and professionals with valid tools to predict hydraulic and water quality in high slope rivers present mostly in the high Andean area of Ecuador.