Simultaneous thin section and phytolith observations of finely stratified anthropogenic deposits from the Neolithic settlement of Çatalhöyük, Turkey, dated between 7400 and 6000 BC provide evidence for both the depositional context and phytolith assemblage of these deposits. Although extracted phytoliths provide a general picture of vegetation that supports existing evidence of a local wet marshland environment, comparisons with observations of phytoliths in situ indicate a diverse range of microcontexts, as well as depositional and post-depositional processes that influence phytolith size. This has implications for studies that use conjoined phytolith size as a proxy for water availability and early agricultural practices. Observations indicate a significant background noise of phytoliths and micro-charcoal in the deposits, linked to the frequent use of fire, which has implications for interpreting assemblages where phytolith counts are low, such as from floors of buildings. This study confirms the usefulness of phytoliths in providing information on human plant use and environment where the taphonomy of the deposits is clear, and provides new evidence for wet farming of at least some of the wheat found at the site. It also suggests there needs to be greater consideration of phytolith taphonomy, which can be provided to an extent by combining phytolith analysis with thin section micromorphology.