High Latitude fjords can serve as sediment trap, bearing different type of proxies, from geochemical to micropaleontological ones, making them exceptional tools for paleoenvironmental reconstruction. However, some unconventional proxies can be present and can be used to depict a comprehensive and exhaustive interpretation of past changes. Here, studying a sediment core in Edisto Inlet (Ross Sea, Antarctica) we used irregular echinoid spines and ophiuroids (Ophionotus victoriae) ossicles to trace environmental changes throughout the last 3.6 kyrs BP. Irregular echinoids can serve as proxy for the organic matter content, while O. victoriae ossicles can be used as proxy for steady sea-ice cycle along with organic deposition events. O. victoriae release a high number of ossicles, making estimation about the population quite challenging; still, presence data, can be easily collected. By applying Generative Additive Models to the stratigraphical distribution of these data, we detected an environmental phase that was previously unnoticed by other traditional proxies: the Ophiuroid Optimum (2–1.5 kyrs BP). In conclusion, here we demonstrate how echinoderm presence can be used as a valuable source of information, while proving the potential of modelling binary data to detect long-term trend in Holocene stratigraphical records.