Shells of intertidal bivalve mollusks contain sub-seasonally to interannually resolved records of temperature and salinity variations in coastal settings. Such data are essential to understand changing land-sea interactions through time, specifically atmospheric (precipitation rate, glacial meltwater, river discharge) and oceanographic circulation patterns; however, independent temperature and salinity proxies are currently not available. We established a model for reconstructing daily water temperatures with an average standard error of ∼1.3 °C based on variations in the width of lunar daily growth increments of Saxidomus gigantea from southwestern Alaska, United States. Temperature explains 70% of the variability in shell growth. When used in conjunction with stable oxygen isotope data, this approach can also be used to identify changes in past seawater salinity. This study provides a better understanding of the hydrological changes related to the Alaska Coastal Current (ACC). In combination with δ18Oshell values, increment-derived temperatures were used to estimate salinity changes with an average error of 1.4 ± 1.1 PSU. Our model was calibrated and tested with modern shells and then applied to archaeological specimens. As derived from the model, the time interval of 988–1447 cal yr BP was characterized by ∼1–2 °C colder and much drier (2–5 PSU) summers. During that time, the ACC was likely flowing much more slowly than at present. In contrast, between 599–1014 cal yr BP, the Aleutian low may have been stronger, which resulted in a 3 °C temperature decrease during summers and 1–2 PSU fresher conditions than today; the ACC was probably flowing more quickly at that time. The shell growth–temperature model can be used to estimate seasonal to interannual salinity and temperature changes in freshwater-influenced environments through time.