A time series data of macrobenthic invertebrates of Valli di Comacchio lagoon (northern Adriatic) from 1996 to 2015, was analysed using Biological Traits Analysis, structural indices, AMBI and M-AMBI indices, with a twofold aim to: firstly, test the resilience of the system, and, secondly, test the influence of climate changes, in terms of temperature and precipitation pattern, on macrobenthic dynamics. Along the studied period macrobenthic community showed marked fluctuations, in terms of richness, diversity, biological traits and ecological groups, which could be related with environmental instability of the lagoon. At the same time, a general tendency towards a deterioration of ecological condition of the lagoon was observed, with a general decrease in species richness, diversity, percentage of sensitive species, and a general increase in the proportion of the more opportunistic trait modalities, such as deposit feeders, burrowing, infaunal and short living animals. Increasing yearly temperature explained only a small part of the variability of macrobenthic community, in terms of biological traits and diversity indices, and this was likely due to the effect of natural fluctuations of environmental parameters and anthropogenic disturbance. Nevertheless, all metrics used are consistent in identifying the response of benthic community to a severe disturbance, likely related with the summer heatwave in 2003. Less marked signs of disturbance were observed also in relations to the thermal anomaly of 2012. Biological Traits Analysis combined with more classical structural and ecological indices, proved to be efficient in identifying temporal changes of the community. Our results suggest that the expected increase in frequency, magnitude and duration of heatwaves could pose serious threat to the resilience capacity of lagoonal macrobenthic community.