Scientists study ancient climate by analyzing tiny fossil shells from ocean sediments, but these chemical records can be altered over time, making them unreliable. We developed new methods to distinguish genuine climate signals from these unwanted changes in 12,000-year-old sediments from the Oregon coast. Using advanced statistical techniques and multiple chemical measurements, we identified which fossil shells preserved original environmental conditions and which had been chemically altered. The alteration follows a predictable pattern: shallow sediments show minor metal contamination, while deeper sediments experience extensive chemical changes from methane-related processes. Different types of fossil shells showed varying resistance to these alterations, with some species preserving original signals better than others. Our integrated approach combines statistical analysis, microscope imaging, and chemical screening to reliably identify unaltered samples. These methods can be applied to other coastal regions worldwide where high biological productivity creates similar preservation challenges. By establishing reliable screening protocols, we help ensure that ancient climate reconstructions accurately reflect past environmental conditions rather than burial-related chemical changes.