Benthic fauna is an important component in marine ecosystems. Due to their relatively sessile habit, benthic macrofauna can serve as an indicator of changes in the marine environment caused by natural or anthropogenic disturbances. This study is primarily focused on the long-term natural variability of the diversity, biotic and multimetric indices, through the use of prolonged data collection (1989-1991 and 2003-2009) on bivalve assemblages in the transitional community of detritic bottoms in the northern Adriatic Sea. With regards to faunistic composition, Cluster and Abundance Comparison analyses were used to assess the recruitment and fluctuations in the quality of bivalve assemblages during the investigated periods. The results of univariate and multivariate analyses clearly distinguished three separate groups (1990-1991, 2003-2006 and 2007-2009) from aforementioned periods during which the research was conducted. Furthermore, this study also discusses the temporal variability in bivalve diversity, which is due to the ecological status of the investigated area in the northern Adriatic Sea.