This study quantifies the degree of pollution and assess the ecological risk of As, Ba, Cd, Co, Cr, Cu, Mo, Ni, Pb, V and Zn in sediments and soils of the Limoncocha Biological Reserve (Ecuador), identified as a Ramsar site with high ecological and socioeconomic value. The hydrologic system of the Reserve is mainly formed by two rivers that drain into the Limoncocha lagoon, which occupies only five percent of the protected area but support a high anthropic influence. Local statistical baseline of studied potentially toxic elements is established using cumulative frequency method, and Al is selected as reference element due to the good correlation with the studied elements. The grade of pollution and the potential ecological risk are evaluated applying three individual (Contamination Factor, Geo-accumulation Index and Enrichment Factor) and six integrated (Degree and modified degree of contamination, Pollution Load Index, Nemerow and modified Nemerow pollution indexes and potential ecological risk index) indices. Results analysis are based on the combined application of traditional statistics, multivariate data analysis and self organizing maps. Outcomes suggest to classify sediments and soils as “moderate contamination and enrichment” due mainly to the concentrations of Cu (66.4–110 mg/kg) and Cd (0.0262–0.808 mg/kg), derived from domestic wastewaters and agricultural activities, and in a lesser extent due to Mo (0.822–4.37 mg/kg), Ni (10.3–25.8 mg/kg), Co (7.27–24.8 mg/kg) and V (60.3–178 mg/kg), derived from oil field drilling activities. The distributions of As (0.328–8.83 mg/kg), Ba (143–1100 mg/kg), Pb (7.20–26.5 mg/kg), Zn (60.1–276 mg/kg) and Cr (10.1–48.6 mg/kg) are heterogeneous in the studied sampling sites. Sediments located next to the pier and at the central area of the Limoncocha lagoon, show moderate potential risk and according to sediment quality guidelines, the calculated mean Effect Range Median quotient (mERMq) classify the sites as medium-low priority risk level. A three-level classification of a mean quotient based on soil quality and soil potential uses is proposed. Soil sites with high anthropogenic activities show low to moderate potential ecological risk being classified as poor soil quality sites but with all potential soil uses allowed according to the legal limits for land uses in Ecuador.