This paper re‐evaluates previous records and adds new data to the relative sea level (RSL; namely the sea level related to the level of the national terrestrial datum) reconstruction in Israel from the last 2400 years based on ancient coastal water wells. Different methods for obtaining the most accurate modern offset between coastal groundwater level and mean sea level are also tested, since this is a crucial component for using wells as reliable sea‐level indicators in the Mediterranean and beyond. Very few, if any, sea‐level studies outside of Israel use coastal wells as RSL indicators; refinements to the methods associated with this indicator type will facilitate their use in other regions. Coastal wells in the study are located within 200 m of the present‐day coastline. The functional age range for the wells is based on site stratigraphy, artifacts, historical records, and the coastal water well typology. These archaeological indicators rely on finding the vertical offset between present‐day coastal groundwater and sea level, and applying it to ancient times. The current study explores two methods to calculate accurate vertical offsets: a) modern averages of the upper aquifer groundwater elevation in the vicinity of ancient wells, which are calculated from 60 years of measurements by the Israeli Hydrological Service; and b) a hydrological model where groundwater elevation is a function of distance from the modern coastline. The model uses a simulation of the coastal aquifer with a two‐dimensional, vertical cross‐section. The modeled approach is found to be preferable. The results show that sea level in Roman times (1st century CE) was similar to present‐day, slightly higher in the Byzantine period (4th to 7th centuries CE), and lower in part of the Early Islamic period (9th to 10th centuries CE). For the later Fatimid/Ayyubid and Crusader periods (11th to 13th centuries CE), RSL reaches its lowest elevations (of about −0.5 m) as previously found. Following these low levels, sea level rose going into the 18th and 19th centuries CE.