Marine environments worldwide are increasingly threatened by warming, deoxygenation, and ocean acidification. Foraminifera may respond to these stressors by altering their test geochemistry and morphology. We integrated morphological features with assemblage and geochemical records of benthic foraminifera from the Danish Straits at the entrance to the Baltic Sea, covering the Last Interglacial period (LIG, MIS5e), to assess potential indications of environmental changes. Using synchrotron radiation X-ray microcomputed tomography (SRµCT), we analyzed Elphidium clavatum in terms of size, surface area, volume, thickness, and pores. Pore patterns and test thickness are evaluated simultaneously to assess both metabolic and mechanical constraints under environmental changes. The initial chamber size (proloculus) may indicate the reproduction mode of foraminifera in response to environmental stress, including salinity and oxygen variations. During the early-mid LIG, the mechanical constraints of E. clavatum remain relatively strong, which are characterized by high pore density, thickness, and low porosity, coinciding with higher bottom water salinity and oxygen content. In the mid-late LIG, the higher porosity, larger proloculus size, lower test thickness and pore density of E. clavatum enhanced the metabolic function and survival rates. These traits reflect adaptation to an increasingly stressful environment with lower salinity and oxygen levels at the Danish Straits, as indicated by declining faunal diversity and increasing E. clavatum abundance. Our study demonstrates that benthic foraminiferal morphological features, including proloculus size, test thickness, and pore patterns, serve as indicators for assessing stress levels and reconstructing bottom water conditions in brackish and potentially hypoxic environments during the LIG.