Waterbird feces (mainly mallard Anas platyrhynchos and coot Fulica atra) were collected from four wetlands in Southern Spain in the field or during capture (n = 558 and n = 59, respectively) to study lead (Pb) shot ingestion. Lead and aluminum (Al) concentrations along with Pb isotope signatures were used to identify sources of Pb exposure. The profile and concentrations of porphyrins and biliverdin in feces were used as biomarkers of toxicological effects. Feces with Pb concentrations ≥ 34 μg/g d.w. showed higher Pb/Al ratios, together with lower (206)Pb/(207)Pb and (208)Pb/(207)Pb ratios, and higher (208)Pb/(206)Pb ratios, than feces with <34 μg/g d.w. Isotope signatures and Pb/Al ratios together indicated that Pb shot ingestion was the likely cause of the high Pb levels in some samples, whereas sediment ingestion was linked to lower/background levels. Coproporphyrin I and protoporphyrin IX were also higher in feces with Pb ≥ 34 μg/g d.w., indicating measurable disruption in heme synthesis. Noninvasive fecal sampling permits study of the degree and source of Pb exposure and physiological effects, with low-effort and minimal disturbance to waterbirds.