CARLIT is a Water Framework Directive-compliant methodology permitting a rapid assessment of water quality using rocky-shore macroalgae as biological quality elements. Here we present the water quality assessment of 32 coastal water bodies of Catalonia (Northwestern Mediterranean) during a period of 14 years (1999–2012) applying CARLIT. The averaged ecological status of the water bodies ranges between high and poor and the Ecological Quality Ratio shows a significant negative relationship with a modified LUSI index, thus providing further evidence on the utility of CARLIT to detect anthropogenic pressures. The lowest interannual variability in water quality was found in water bodies having most of their shore covered by natural rocks, while the highest variability was observed in water bodies situated in semi-confined environments or located close to freshwater discharges. In spite of the multiple advantages of CARLIT as a monitoring methodology, it can show strong disagreements in water quality assessment with other methodologies using other biological quality elements (i.e., macroinvertebrates). These discrepancies mainly occur in water bodies with reduced extension of rocky shores, questioning the use of CARLIT in these situations.