Fish are a protein source for many people in Colombia. However, environmental pollution of some aquatic ecosystems may pose health risks to humans. The aim of this study was to assess the levels of total mercury (T-Hg) in muscle and their relationship with nematode infections in fish from Dique Channel, a freshwater ecosystem located Northern Colombia. Eight hundred ninety fish specimens belonging to 13 different species were collected. T-Hg concentration was measured using atomic absorption spectroscopy, previous electrothermal atomization. Nematodes were identified as Contracaecum sp. Species such as Hoplias malabaricus and Sorubim cuspicaudus presented the highest values for Hg and parasite infection (0.09 ± 0.01, 0.12 ± 0.02 μg/g; prevalence 100, 100 %, respectively), whereas the lowest were detected in Prochilodus magdalenae (0.02 ± 0.002 μg/g; 0 %). Pooled data revealed a high correlation between trophic level and parasite abundance (ρ = 0.771; P = 0.002) as well as with T-Hg (ρ = 0.786; P < 0.001). The overall correlation between parasite abundance and T-Hg was moderately to low but positive (ρ = 0.217; P < 0.001). However, when individual species were considered, pair relationships between parasite abundance, morphometric parameters, and Hg concentration, varied between positive and negative values. These data suggest the presence of nematodes is determined by the trophic level of the fish species, similarly to what occurs with Hg. Moreover, the co-occurrence of these two stressors involves different types of interactions with morphometric variables that are species-specific. These observations open new doors to the understanding of the interaction between chemical pollutants and organisms.