Abstract Anomalously cold conditions in the tropical Pacific, related to a strong La Niña event, affected numerous countries in 2010. Several areas in Colombia were severely impacted, including agricultural fields in La Mojana floodplain that were completely flooded for almost 2 years. This study assesses the effects of flooding on the levels, spatial distribution, and sources of trace metals in 222 agricultural topsoils of this floodplain. Our results show that mean concentrations of Cu 48.4 mg kg −1 (11–103 mg kg −1 ), Zn 79.2 mg kg −1 (6–207 mg kg −1 ), Ni 58.1 mg kg −1 (17–101 mg kg −1 ), Pb 3.2 mg kg −1 (0.13–14 mg kg −1 ), Cd 0.56 mg kg −1 (0.05–1.4 mg kg −1 ), Mn 411 mg kg −1 (55–1,277 mg kg −1 ), and Hg 0.10 mg kg −1 (0.05–0.22 mg kg −1 ) were higher than the world's averages. Topsoils revealed different degrees of pollution depending on the metal, of which Pb was the most problematic element, with 82% of the soil samples classified as heavily contaminated. Principal component analysis suggests that soil contamination was primarily derived from poor agricultural practices and contaminated river overflows from upstream mining areas. Our results show that an extreme flood event might increase the bioavailability of metals (especially Pb) for crops in most (66%) of the agricultural soils, posing a potential threat to human health.