Shells of bivalves potentially provide an excellent archive for high-resolution paleoclimate studies. However, quantification of environmental variables, specifically water temperature remains a very challenging task. Here, we explore the possibility to infer water temperature from changes of microstructural characteristics of shells of the common cockle, Cerastoderma edule. The size and elongation of individual microstructural units, i.e., prisms, in the outer shell layer of seven three to five year-old, specimens collected alive from the intertidal zone of the North Sea near Texel, The Netherlands, and Schillig, Germany, were measured by means of automatic image processing. Growth patterns (circatidal, ciralunidian and fortnightly increments and lines), shell oxygen isotope values and mark-and-recovery experiments were used to place the shell record in a precise temporal context. Irrespective of the locality and ontogenetic age, size and elongation of the prisms increased non-linearly with water temperature. Small (0.12 ± 0.05 μm2) and round prisms (elongation: 2.42 ± 0.31) were formed at temperatures of ca. 10 °C (late April), whereas larger (0.33 ± 0.11 μm2) and more elongated prisms (3.26 ± 0.28) occurred during hot summer (ca. 22 °C). No clear-cut or consistent correlation existed between microstructural characteristics and growth rate as well as a variety of other environmental variables such as salinity, chlorophyll a and turbidity. Based on these findings, a model was constructed from three shells at Texel that enables reconstruction of water temperature with a precision of 1.7 ± 1.0 °C from prism size and elongation: SST = 9.02 + 17.25 Ps + 1.10 Pe. This model was successfully tested at four shells from Schillig. The new temperature proxy can be of particular interest for paleoclimate studies in nearshore settings when non-recrystallized C. edule shells are available. Future studies are required to verify our findings and check if other species with the same and different microstructures show similar relationships with water temperature.