Benthic monitoring programs are therefore useful to assess local effects of contamination (Borja et al., 2008). Several studies applying biological tools to assess pollution in enclosed or semi-enclosed ports have been developed worldwide (Dauvin et al., 2010 and references therein). However, there are still few studies along the coastal areas of South America that integrate the analysis of chemical parameters and biological multivariate data (Guerra-García et al., 2003 and Venturini et al., 2008).