Abstract Indentation measurement has emerged as a widely adapted technique for elucidating the mechanical properties of soft hydrated materials. These materials, encompassing gels, cells, and biological tissues, possess pivotal mechanical characteristics crucial for a myriad of applications across engineering and biological realms. From engineering endeavors to biological processes linked to both normal physiological activity and pathological conditions, understanding the mechanical behavior of soft hydrated materials is paramount. The indentation method is particularly suitable for accessing the mechanical properties of these materials as it offers the ability to conduct assessments in liquid environment across diverse length and time scales with minimal sample preparation. Nonetheless, understanding the physical principles underpinning indentation testing and the corresponding contact mechanics theories, making judicious choices regarding indentation testing methods and associated experimental parameters, and accurately interpreting the experimental results are challenging tasks. In this review, we delve into the methodology and applications of indentation in assessing the mechanical properties of soft hydrated materials, spanning elastic, viscoelastic, poroelastic, coupled viscoporoelastic, and adhesion properties, as well as fracture toughness. Each category is accomplished by the theoretical models elucidating underlying physics, followed by ensuring discussions on experimental setup requirements. Furthermore, we consolidate recent advancements in indentation measurements for soft hydrated materials highlighting its multifaceted applications. Looking forward, we offer insights into the future trajectory of the indentation method on soft hydrated materials and the potential applications. This comprehensive review aims to furnish readers with a profound understanding of indentation techniques and a pragmatic roadmap of characterizing the mechanical properties of soft hydrated materials.