Time-series δ18O and δ13C records from cohabiting massive coralPorites australiensis and giant clamTridacna gigas from the Great Barrier Reed of Australia, and from calcareous green algae in a core through modernHalimeda bioherm accreting in the eastern Java Sea, provide insights into the complex links between environmental factors and stable isotopes imprinted in these reef skeletal materials. The aragonitic coral and giant clam offer 20 years and 15 years of growth history, respectively. The giant clam yields mean δ18O and δ13C values of-0.5±0.5‰ and 2.2±0.2‰ (n=67), which agree well with the predicted equilibrium values. The coral yields mean δ18O and δ13C values of-5.6±0.5‰ and-1.8±0.7‰ (n=84), offering a striking example of kinetic and metabolic fractionation effects. Although both the coral and giant clam harbor symbionts and were exposed to a uniform ambient environment during their growth histories, their distinct isotopic compositions demonstrate dissimilar calcification pathways. The δ18O records contain periodicities corresponding to the alternating annual density bands revealed by X-radiography and optical transmitted light. Attenuation of the δ18O seasonal amplitudes occurring in the giant clam record 8 years after skeletal growth commenced is attributed to a changeover from fast to slow growth rates. Extreme seasonal δ18O amplitudes of up to 2.2‰ discerned in both the coral and giant clam records exceed the equivalent seasonal temperature contrast in the reef environment, and are caused by the combined effect of rainfall and evaporation during the monsoon and dry seasons, respectively. Thus in addition of being useful temperature recorders, reef skeletal material of sufficient longevity, such asPorites andTridacna, may also indicate rainfall variations. Changing growth rates, determined from the annual growth bands, may exert a primary control on the coral δ13C record which shows a remarkable negative shift of 1.7‰ over its growth history, by comparison with only 0.15‰ negative shift in the contemporaneous giant clam record. Use of coral δ13C records as proxies of fossil fuel CO2 uptake by the ocean must be regarded with caution. The δ18O and δ13C records fromHalimeda are remarkably uniform over 1000 years of bioherm accretion history (δ18O=-1.7±0.2‰; δ13C=3.9±0.1‰,n=28), in spite of variable Mg-calcite cements present in the utricles. Most of the cement infilling is probably syndepositional, and both theHalimeda aragonite and the Mg-calcite cements containign 12.3 mole % MgCO3 are deposited in isotopic equilibrium. Therefore, in favorable circumstances these algal skeletal remains may act as the shallow water analogs of benthic foraminifera in deep sea sediments in recording ambient sea water isotopic composition and temperature.