The environmental health of Buenaventura Bay, a highly impacted tropical estuary, is influenced by numerous human activities, including mining upstream. Large-and small-scale fishing plays an important role in the local economy, so we investigated the dynamic processes of bioaccumulation of mercury at basal trophic levels. Four samples were taken at each of the four locations in Buenaventura Bay during each of the four seasons of 2015. We measured the total mercury content (T-Hg, dry weight) in sediments and in muscle tissue across 17 macroinvertebrate species. The most abundant were the blue crab (C. arcuatus) and the mantis shrimp (S. aculeata aculeata). Blue crab showed an average muscle T-Hg value exceeding the limit of 0.2 g•g-1 , which is the maximum T-Hg level suggested for food consumption by vulnerable humans and populations: pregnant women, children, and the community that feeds from this source of protein on a daily basis. It was found that, 6.22% of individuals exceeded the 0.5 g•g-1 level, which is the maximum T-Hg level suggested for food consumption by the general population: the population that consumes it sporadically. Significantly high values of T-Hg in blue crab and mantis shrimp occurred during low salinity conditions in the estuary, suggesting that Hg mainly originates from river runoff during the rainy season. Nevertheless, the biota-sediment accumulation factor (BSAF) was favored in high salinity, which could mean greater availability of Hg for higher levels of the estuarine food web in the dry season and in marine waters. In general, the T-Hg levels in some samples exceeded 0.2 g•g −1. Therefore this pollutant must be monitored due to its biomagnification potential and as a threat to human health, especially that for the local population of fishermen and their families.