Worldwide, the impacts caused by anthropic activities on the functioning of rivers can be aggravated by climate change, mainly due to intense droughts. In addition, the growing demand for water resource, particularly in low -flow periods, has caused an increase in the number of hydraulic barriers for water collection to meet these demands without considering negative impacts on ecosystem services. In Ecuador, current legislation does not contribute properly to leaving a minimum flow in periods of greater water stress of rivers strongly affecting their operation. Thus, the general objective of the project is to establish the effect of the alteration of the flow and the respective water stress on the communities of Macroinvertebrates aquatic of the sub -basins of the Yanuncay and Tomebamba rivers, the same ones that supply the city of Cuenca. The following results are expected to obtain determining hydraulic variables in the spatial and temporal distribution of aquatic communities in the periods of greater water stress; (Ii) Hydraulic characteristics of habitats by hydrodynamic modeling; (Iii) distribution of the suitable habitats of the communities of Macroinvertebrates; And (iv) validation of the use of objective species, determined in a previous research project. The information that is expected to generate is essential for the subsequent esteem of the environmental flow for the Yanuncay and Tomebamba rivers.