We used a Tridacna squamosa (Tridacnidae, Bivalvia) shell that lived between 2006 and 2012 to reconstruct environmental conditions in South East Sulawesi (Indonesia). We focused mainly on estimating the influence of temperature and rainfall on the shell geochemistry, as well as ENSO anomalies. Comparison of the measured and theoretical δ18O values show clear seasonal variations and confirms that this species secretes its shell at isotopic equilibrium. The δ18O in T. squamosa shows how the increased rainfall associated with monsoon precipitations in this area influences the δ18O shell signal during the rainy season, the correlation between shell δ18O and SST (r2 = 0.62) decrease in warm/wet seasons (SST > 28.5 °C). Shell Mg/Ca profiles presents better correlation with SST (r2 = 0.8) than Sr/Ca profiles (r2 = 0.52). Shell Ba/Ca ratio increases during each dry season when primary productivity is maximum. Secondary Ba/Ca peaks also occur during the certain wet seasons and appear associated with abnormal enhanced runoff. Shell δ13C co-varies with primary productivity and salinity, with highest δ13C values occurring during the dry seasons. During 2010–11, abnormal values were detected in all geochemical proxies as result of the strong La Niña event. This calibration study demonstrates the ability of T. squamosa shells to accurately reflect present day environmental processes with seasonal resolutions and to define the local signature of hydrological changes associated with ENSO.