Abstract In this study we propose a conceptual framework, i.e. the Monitoring Breakdown Structure (MBS) as a tool for the management of marine ecosystems. The conceptual framework thinks through the complexity of marine ecosystems keeping into account the variety (space) and variability (time) dimensions. Consistently with the MBS we have built the control charts of trace metal concentrations of two selected biomonitors in the Beagle Channel (south Patagonia) (case study). Thus, we have tested the aptitude of two species of mollusks as biomonitors of heavy metal (HMs) pollution. The selected species were the limpet Nacella (P) magellanica and the bivalve Mytilus chilensis. Seven hundred eighty-five samples were collected along 170 km of the coastal area of the Beagle Channel (BC), (Tierra del Fuego, Argentina) in seven selected georeferenced locations and four sampling campaigns (2005, 2007, 2011, 2012). Cd, Cr, Cu, Ni, Pb and Zn determinations in seawater and mollusks by atomic absorption spectrometry (AAS) were carried out. The calculation of the respective concentration factors (CFs), i.e. their capacity as strong bioaccumulators, was also conducted. This is of relevance because it aims to use these data as a baseline reference for other geographical areas. Second, we have compared metal bioaccumulation differences among sites and the contamination trend by building, for the first time, the control charts of the baseline metal concentrations in the biomonitors. For these purposes, we applied probabilistic Johnson's method. Furthermore, the control charts (based on four years baseline data) allowed us to test the contamination trend by plotting data from 2012 vs 2011. Our results confirm N. magellanica as an extremely strong accumulator of Cd, and M chilensis strong bioaccumulator of Cd and Zn. Zn was the most abundant metal followed by Cu. Overall, regarding the contamination trend, based on thousands of determinations we observed that the six mean metal levels were quite constant over time. Moreover, metal distribution among sites turned out to be not univocal (no one site is more contaminated than the other sites). Thus, the expected hypothesis of Ushuaia Harbour as being the most contaminated site should be reconsidered. This reinforces the hypothesis of our data as baseline data (except for cadmium), that should be considered in management decisions about future environmental monitoring programs, i.e. preventing/managing marine accidents.