Benthic macroinvertebrates, macroalgae and phytoplankton constitute the Biological Quality Elements (BQE) proposed in the Water Framework Directive (WFD, 2000/60/EC) to be used for the classification of the ecological status of a water body. Chlorophyll-a is a usefull expression of phytoplankton biomass and this indicator is an effective and relevant BQE for coastal ecosystems which is universally accepted. In the present study, interpretations of the class boundaries according to normative definitions of WFD, are presented for chlorophyll-a in South Eastern (SE) Black Sea. Water quality classification was determined in five different categories as "high, good, moderate, poor and bad". The coastal waters of SE Black Sea were classified in 8 different typologies (K1-K8) based on depth, salinity and substratum types. In this study, types K1 and K2 (>17,5 salinity, >30m depth) were considered because of availability of time-series data for those typologies. Sinop and Surmene sites were selected due to the best available long-term chlorophyll-a data set, respectively over the period of 2002-2010 and 2001-2011 for chlorophyll-a respectively. Type specific chlorophyll-a (Chl-a) reference and threshold values were determined based on the 90th percentile of the long-term collected chlorophyll data set. Due to the high seasonal variability of phytoplankton biomass, the annual values were not considered adequate and the classification tool was developed on seasonal basis. The High/Good (H/G) and Good/Moderate (GM) boundaries were defined as seasonal from the long term data sets for Surmene and Sinop sites. All the boundaries were higher at the Sinop site. Ecological quality ratios distributed between 0-1. It would be necessary to underline the fact that these class boundaries might be higher for waters where depths are below 30 m and salinity values are less than 17.5. However, there is not enough data to support this assumption for the near coast waters of the SE Black Sea. Eventhough Chl-a scaling can not be used as a single tool for the ecological quality classification it is a reliable approach to use the obtained boundaries at temporal and spatial scales for the quality classification of SE Black Sea waters above 30 m depth.