Cultural eutrophication is the leading cause of water quality degradation worldwide. The traditional monitoring of eutrophication is time-consuming and not integrative in space and time. Here, we examined the use of carbon (δ13C) and nitrogen (δ15N) isotopic composition to track the degree of eutrophication in a bay of Lake Titicaca impacted by anthropogenic (urban, industrial and agricultural wastewater) discharges. Our results show increasing δ13C and decreasing δ15N signatures in macrophytes and suspended particulate matter with distance to the wastewater source. In contrast to δ15N and δ13C signatures, in-between aquatic plants distributed along the slope were not only affected by anthropogenic discharges but also by the pathway of carbon uptake, i.e., atmospheric (emerged) vs aquatic (submerged). A binary mixing model elaborated from pristine and anthropogenic isotope end-members allowed the assessment of anthropogenically derived C and N incorporation in macrophytes with distance to the source. Higher anthropogenic contribution was observed during the wet season, attributed to enhanced wastewater discharges and leaching of agricultural areas. For both seasons, eutrophication was however found naturally attenuated within 6 to 8 km from the wastewater source. Here, we confirm that carbon and nitrogen stable isotopes are simple, integrative and time-saving tools to evaluate the degree of eutrophication (seasonally or annually) in anthropogenically impacted aquatic ecosystems. Display omitted •C and N stable isotopes were measured in four compartments of Lake Titicaca.•Anthropogenic discharge affects baseline C and N isotope signatures.•C recycling from soil, anthropogenic and lacustrine sources affect the δ13C signature.•δ15N signatures track anthropogenic contamination independently of plant type.•Decreased anthropogenic contribution in the bay assessed by isotope mixing model.