Cultural heritage often brings to mind elements like sculptures, paintings, monuments, and buildings as well as archeological objects. Today, underwater heritage and its surrounding environment are also considered part of cultural heritage because communities identify themselves with the natural landscape. This study is focused on a shipwreck belonging to the second half of the 15th century that was discovered in 1998 by chance in the sediments of the Urdaibai estuary, in Urbieta (Gernika, Basque Country), at 4 m underground. A scientific study presented in this work was performed, as this archeological site was absolutely out of context and in need of a preservation and conservation procedure. Therefore, our aim was to shed light on the origin of the shipwreck and to assess the conservation state to develop a precise conservation plan. Pursuing this objective, a first analysis on three selected groups of iron nails was performed, looking at the raw materials and degradation patterns through the knowledge of the alteration compounds. By means of nondestructive analytical techniques such as Raman spectroscopy and X‐ray fluorescence, the presence of iron, zinc, and silicon was detected in the outer layer of the iron samples. The analysis of the nails and wood of the shipwreck confirmed that the presence of zinc in the pieces indicates an important impact of the contaminated sediments deposited in the last 80 years on the upper part of the burial in which the shipwreck was located.