This paper presents the first paleoenvironmental reconstruction of the last 1,130 a of the Marriaga Swamp in the Atrato River delta in northwestern Colombia. The geochemical analyses of a 220 cm sediment core retrieved from the swamp reveal interesting climatic episodes and sedimentary changes in the last millennium. We split the core into three segments, according to sediment features, organic carbon content (OC), and geological ages. Records show different alternations of humid and dry periods, biological productivity, carbonate precipitation, weathering grade, and high heavy metal concentrations. The segments also concur with the geochemical differences determined by (Zr+Rb)/Sr, Ca/Ti Mn/Fe, OC/Ti, Mg/Ca Ba/Al, Sr/Al, and Ca/Al ratios. The older sequence (between 1,130 ± 90 a and 870 ± 70 a) shows a dry period with intermittent flooding events and high OC production in subareal conditions, followed by a more humid environment between 870 ± 70 a and 530 ± 40 a, with depletion of trace element ratios and OC. The more recent period (530 ± 40 a to present) evinces an environment dominated by the fluvial regime, based on a lower Ca/Al ratio and a rise of OC. The statistical correlations display three main clusters that distinguish among organic-biological productivity, bedrock source components, and heavy metal inputs.