Soundscape acoustic components are dynamic, changing through time and space. Habitat structure plays a principal role in soundscapes; however, it is unknown whether autogenic ecosystem engineers (AEE), which modify the habitat with their structures, have a primary role in soundscape dynamics. The Mar Chiquita coastal lagoon, a biosphere reserve, is the Argentinean primary invasion site of the invasive AEE polychaete Ficopomatus enigmaticus. This species forms enormous calcareous aggregates (“reefs”) that are known to have numerous effects on the community structure and dynamics. The objective of this study is to evaluate whether there is a pattern in Mar Chiquita coastal lagoon underwater soundscapes associated with the presence of F. enigmaticus reefs. Acoustic data were collected seasonally in two adjacent areas, one rich in reefs and another reef-free area. Combining manual screening of spectrograms with automatic analyses, the presence/absence of biological and geological signals and temporal changes were determined. Preliminary results showed that there was greater abundance and richness of biophonic activity in the reef, while geophonic signals were more abundant in the reef-free area. Knowledge of these acoustic shifts can contribute to understanding how natural communities respond to environmental change due to an ecosystem engineer, while also providing valuable insights for coastal conservation.