Seasonally resolved records of carbon and oxygen isotopic composition (δ18O) in fossil shells of giant clams (Tridacnidae) recovered from the Kogachibaru Shell Mound (26°26′N, 127°49′E) and the Second Aragusuku‐Shichabaru Ruin (26°18′N, 127°46′E) in Okinawa‐jima, southwestern Japan, were investigated to reconstruct subtropical coral reef environments of the past. The samples, mainly composed of aragonite shells with limited amounts of diagenetically‐altered calcite cements, were selected for geochemical analyses. The radiocarbon dating of the samples for stable isotope analyses yields about 4000 yr cal. BP for the Kogachibaru Shell Mound and about 1900–1700 yr cal. BP for the Second Aragusuku‐Shichabaru Ruin, respectively, that correspond to the early and middle Shell Mound periods in Okinawa‐jima. These show good agreement with the respective ages inferred from excavation. The shell δ18O values roughly show seasonal variations, coincident with the occurrence of annual growth bands. Applying corrections for the effect of diagenetic alteration, the averages of annual, summer, and winter δ18O values of fossil shells were significantly lower (by 0.1–0.7‰) than those of aragonite theoretically precipitated in present‐day coral reef water of Okinawa‐jima. These results demonstrate that annual mean seawater temperature and salinity at the sites where the Tridacnida spp. lived were about 1–3°C higher and/or about 1–2 lower than at present. This variation cannot be fully explained by global climate change, sea level change, and topographic growth of coral reef. Therefore, it is likely that the giant clams lived in extremely small and/or closed coral‐reef lagoons with less water circulation where seawater is highly susceptible to insolation‐induced temperature increase and input of fresh water; the effect could be enhanced by the fisheries lifestyle that stonewalling would be constructed at shallow waters through the use of tidal variation during the early and middle Shell Mound period in Okinawa‐jima.