Temporal variability is widely acknowledged as a main source of uncertainty and error in ecological studies. Despite this, conservation management tends to overlook the temporal dimension of ecosystems due to financial and operational constraints. The main aim of this study is to identify potential biases in the implementation of the European Water Framework Directive due to temporal variability in waterchemistry parameters. Specifically, we focused on the establishment of water-bodies typologies and the assessment of water quality in transitional waters. We measured waterchemistry (salinity and nutrients) in 34 coastal lagoons on a monthly basis over a full year (March' 08-February' 09) in a Mediterranean archipelago (Balearic Islands, Spain). We found large differences in nutrient levels among both the coastal lagoons of different islands (Majorca, Minorca, Ibiza and Formentera) and lagoons of different salinity types (euhaline, mesohaline and oligohaline). From an applied perspective, our results show that monthly values were inadequate for determining salinity-based typologies, as lagoon salinity values varied widely from month-to-month. Additionally, we found a lack of agreement between ecological assessments based on invertebrates and those based on nutrient thresholds often used for transitional waters. These facts highlight the need for a definition of specific thresholds for coastal lagoons which are not currently available.