The work was to propose the flux of Carbon Dioxide in the water-atmosphere interface, the flux of Particulate Organic Carbon associated with sediment, the flux of Particulate Organic Carbon based on litter fall and the flux of Dissolved Organic Carbon in the subsurface zone as ecohydrological indicators that support decision-making from the standpoint of vulnerability analysis of watersheds under dams construction. A comparison between conventional and proposed methodologies for the identification of environmental impacts was made. It was proposed and described ecohydrological indicators, taking into account processes associated with nutrient cycles, specifically the carbon cycle. Finally, It was discussed the applicability of the indicators within a vulnerability analysis methodology which was appropriated and consistent with the ecohydrological philosophy. The results indicate that conventional methodologies for identifying environmental impacts need to be improved because, although their application may be useful for other projects, in the case of dam construction, these methodologies do not have enough predictive tools of the behavior of a complex system like a watershed. Therefore, this proposal was based on ecohydrological indicators that reflect an integrated functioning point of view of watersheds which potentially will be used in the development of vulnerability analysis of watersheds in turn, those which will help to improve the environmental impact assessments (EIAs ) for the construction of dams.