The influence of salinity and water chemistry on Mg/Ca, Sr/Ca and Ba/Ca ratios in the aragonitic shells of the Manila clam were investigated. Clams were reared at constant temperature (20 °C) under different controlled conditions of salinity, commonly encountered in their natural habitat. Clams were held in three tanks with a constant salinity of 35 for the first 35 days and then two tanks were changed to lower salinities (20 and 28) for the next 29 days. Individual shell Mg/Ca, Sr/Ca and Ba/Ca ratios were studied through time. Despite stable conditions (temperature, salinity, and Mg/Cawater) for clams reared at salinity 35 during the experiment, Mg/Ca shell ratios increased through the time. Moreover the salinity decrease at t35 slowed the increase of Mg/Ca shell ratios at salinity 28 and resulted in a Mg/Cashell decrease at salinity 20, despite similar Mg/Cawater ratios in the different salinity treatments. Microprobe analyses illustrate that Mg varies along contemporaneous growth lines. The variable shell Mg/Ca ratios suggests that incorporation of magnesium into shell carbonate is strongly regulated by the organism and not by environmental conditions. Interestingly, microprobe analyses illustrated that Mg was not associated with shell sulfur as other studies have suggested. Sr/Ca shell ratios of clams reared at salinity 35 and under constant conditions were also not as constant as expected if Sr/Ca ratios were an environmental proxy. There was an inverse correlation between shell Sr/Ca and salinity despite a slight positive correlation between salinity and Sr/Ca ratios of the water, indicating that Sr/Ca ratios do not reflect environmental conditions. A strong inverse correlation between salinity and Ba/Ca shell ratios (and a positive correlation between Ba/Ca shell and Ba/Ca water) was observed. Therefore, Ba/Ca shell ratios seem to be a promising proxy of high-resolution (1 day) salinity variations in estuarine waters (via the relationship between Ba/Ca water and salinity). This study clearly illustrates that both Mg/Ca and Sr/Ca ratios in aragonite shells are not under environmental control and that Ba/Ca ratios are, with the later tracking high-resolution water Ba/Ca ratios and hence estuarine salinity variations.