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Eutrophication is a globally significant challenge facing aquatic ecosystems, mostly associated with human induced enrichment of these ecosystems with nitrogen and phosphorus. Given the complexity of assigning eutrophication issues to local primary N sources in field-based studies, this paper proposes a multi-stable isotope and biological framework to track nitrogen biogeochemical transformations, inputs and fate of nitrate in groundwater-dependent shallow lakes. Three representative freshwater ecosystems from the Pampa Plain (Argentina), with different land uses and topographic features were selected. Groundwater (N = 24), lake (N = 29) and stream (N = 20) samples were collected for isotope (δ 15 N-NO 3 - and δ 18 O-NO 3 - , δ 18 O-H 2 O) and hydrogeochemical (major ions and nutrients) determinations, and in the case of surface water, also for biological determinations (chlorophyll-a, fecal coliforms and nitrifying bacteria abundance). Both chemical and isotopic characteristics clearly indicated that denitrification was limited in lakes and streams, while evidence of assimilation in shallow lakes was confirmed. The results suggested that groundwater denitrification plays a role in the nitrate concentration pattern observed in the Pampeano Aquifer. The proportional contribution of nitrate sources to the inflow streams for all years were estimated by using Bayesian isotope mixing models, being ammonium nitrified in the system from soil and fertilizers ~50 - 75 %, sewage/manure ~20 - 40 % and atmospheric deposition ~5 - 15 %. In this sense, agricultural practices seem to have a relevant role in the eutrophication and water quality deterioration for these watersheds. However, limnological, bacterial and algal variables, assessed simultaneously with isotopic tracers, indicated spatio-temporal differences within and between these aquatic ecosystems. In the case of Nahuel Rucá Lake, animal manure was a significant source of nitrogen pollution, in contrast to La Brava Lake. In Los Padres Lake, agricultural practices were considered the main sources of nitrate input to the ecosystem., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier B.V. All rights reserved.)