Methodologies developed by European Member States to assess the environmental quality of their coastal waters under the EU Water Framework Directive (WFD, 2000/60/EC) may have an associated source of uncertainty. Here we identify and quantify the level of uncertainty in the CARLIT (Cartography of littoral and upper-sublittoral communities) methodology to test its effectiveness and reliability. The outcomes show that the effect of temporal variability (among years) within each water body is low when CARLIT is performed every year along the entire rocky coast. The spatial variability within a water body is also low. According to these results, CARLIT could be performed every 3 years across all the water body or, alternatively, every year considering at least 60% of each water body, without a significant reduction of the confidence in the classification of the Ecological Quality Status (EQS).