Geographical and temporal changes of total mercury (T-Hg) concentrations in sediments, macrophytes and fish were evaluated in the Ayapel Marsh, Mojana, Colombia. Sampling was conducted during 2006-2007, including both rainy and dry seasons, and T-Hg was measured using atomic absorption spectroscopy. Distribution of T-Hg in sediments and the macrophyte Eichhornia crassipes showed that higher concentrations were found along the flooding pathway of the Cauca River. Hg has also polluted the food chain. Highest T-Hg concentrations in fish were detected for the carnivorous Pseudoplatystoma fasciatun (0.432 ± 0.107 μg/g, fresh weight [fw]), and lowest in the non-carnivorous Prochilodus magdalenae (0.143 ± 0.053 μg/g, fw), with differences between trophic levels. T-Hg for fish samples (0.298 ± 0.148 μg/g, fw) did not exceed the limit consumption level (0.50 μg/g, fw). It is concluded that mercury-polluted sediments from the Cauca River, contribute to Hg deposition into the Ayapel Marsh. Accordingly, interventions must be conducted to decrease Hg accumulation in fish.