To correctly dimension rehabilitation actions for eutrophic water bodies, reactive carbon (C) loads from hydrological basins to lakes and reservoirs must be evaluated. These loads result from emissions and transport of C from both natural sources and human activities that occur in watersheds, where C is emitted from point and non-point sources, and participate in attenuation processes during its transport to lakes and reservoirs. The Valle de Bravo reservoir is a eutrophic lake located in central Mexico, and is actually being used for tourism and as part of the Cutzamala system drinking water supply to the Valley of Mexico Metropolitan Area. To obtain adequate water quality for these uses, rehabilitation actions are needed both in the water body and the hydrological basin. To determine and propose emission reduction scenarios and decreased reactive C loads to the Valle de Bravo reservoir, the transport of C from the emission sources in the basin were assessed through an emissions inventory and application of a reactive C transport. Modeling results were verified with field observations and five different C-reduction scenarios were evaluated, including decreases in wastewater emissions, livestock production, and fish farming. Total reactive C emissions was estimated in 891 t yr−1, from which around 60% were attenuated, and 40% transported to the reservoir. Higher decrease in external C loads were obtained with reduced emissions from livestock activities. The results highlight the importance of evaluating both diffuse and point source emissions as well as natural attenuations when evaluating transport of reactive C to water bodies. The outcomes counterproof paradigms that are common in this part of the World that consider urban wastewater treatment as the all-inclusive solution to water quality problems and lake restoration activities. Carbon loads should be reckoned for each case, related to the various emission sources, and to the basin characteristics so that sustainable lake restoration activities can be developed and implemented.