The community metrics chosen generally had robust statistically significant associations with both physicochemical and contaminant variables, which supports the ecological relevance of these parameters as indicators of aquatic environmental health. Within the study area, the shoal flounder and their parasites live in a polluted environment with relatively high levels of hydrocarbons and nitrate. Regarding nitrate, we emphasise that if uncontrolled sewage discharge continues in the southern Gulf of Mexico, hypoxic conditions similar to those caused by the Mississippi river can be expected in the near future.