© 2017 Elsevier Inc. Forty nine sediment samples were collected [Upstream section: Zahuapan River (1–12) and Atoyac River (13–20); Confluence Zone (21–31); Valsequillo dam (32–49)] to investigate the geochemical sources, enrichment, contamination and ecological risks of metals in the fluvial sediments of Atoyac River basin, an area experiencing tremendous urban and industrial development in Central Mexico. The sediments were analyzed for 23 major (Al, Fe, Ca, Mg, Na, K, P, S & Ti) and trace (Ba, Mn, As, Co, Cr, Cu, Mo, Ni, Pb, Sc, Sr, V, Zn & Zr) acid leachable metals (ALMs). The grain size results revealed that the sand fraction of sediments accounts for 53.1% and silt for 46.9% respectively. The concentration pattern (avg. values) shows a spatial distribution of metals in the four zones indicating that S (0.10; 0.13; 0.34; 0.80 in %), Ca (0.96; 0.73; 4.98; 1.85 in %), P (0.05; 0.05; 0.16; 0.08 in %), Cr (122; 182; 111; 104 in µg g−1), Mo (5; 9; 6; 10 in µg g−1), Cu (13; 14; 53; 29 in µg g−1), Ni (19; 22; 29; 46 in µg g−1), Pb (9; 12; 21; 14 in µg g−1), Zn (92; 62; 204; 92 in µg g−1) & As (2.63; 2; 3.35; 4.49 in µg g−1) exceeded the local background values primarily attributed to the natural volcanic inputs. Geochemical indices such as enrichment factor (EF), geoaccumulation index (Igeo) and pollution load index (PLI) were used to assess the degree of metal enrichment and the results revealed significant external influences over some metals (As, Cu, Pb and Zn). The calculation of potential ecological hazards index showed that among 23 tested metals, As, Pb, Cu, Ni and Cr were the main potential risk factors that will cause harmful biological effects in the riverine environment. A new complementary approach which integrates metal contamination, enrichment and ecological risks aided in more accurate determination of metal sources and their environmental impacts. Multivariate statistical analysis revealed the groupings of elements as lithogenic (Al, Fe, Ca, Mg, Na, K, P, S, Ti, Ba, Mn, Co, Cr, Ni, Sc, Sr, V & Zr) and external (Cu, Pb, Zn, Mo & As) suggesting that the metal sources are from volcanic events, natural weathering processes and the industrial influences from the Puebla City.