An ecological survey of the benthic communities was carried out, at both spatial and temporal scales, in Papapouli Lagoon, the first ecotouristic park in Greece by applying for the first time, ecological network analysis. The application of ecological network analysis provided novel information on the quality of interactions among species, undetected by the most frequently used methods. The sorting of substrate samples enabled the identification and density determination of 40,036 individuals belonging to 31 different taxa, although, strong dominance of only a few species was observed. "Deposit feeders" were the dominant trophic group in all sampling sites and seasons while "suspension feeders" exhibited relatively the lowest abundance. The periodic opening of the sea inlet seems to be of crucial importance. In coastal lagoons, where there is constant communication with the sea, benthic fauna patterns seem to change according to the sea-land gradient. However, in intermittently closed lagoons, such as Papapouli Lagoon, a more homogenous pattern is evident. The obtained networks showed that when communication with the sea is interrupted all the benthic fauna patterns tend to be destabilized and centralized around one species, which in most cases is a "deposit feeder". When the inlet opens and communication with the sea is restored, the benthic composition seems to be more cohesive, especially in the most distant regions. Knowledge generated by network analysis should provide a valuable tool in order to assess potential environmental changes and assist management decisions.