Variabilities of temperature and salinity over Long Island Sound (LIS), New York, are examined using observations from 1991 to 2002. There is a strong seasonal variation in the temperature, and its interannual variability is characterized by a higher variance during winter than summer. The salinity exhibits regular seasonal patterns driven by freshwater input, but there is a long-term change throughout LIS. Anomaly maps of temperature and salinity indicate strong longitudinal gradients increasing in the westward direction. Empirical orthogonal function analyses indicate that the first modes of temperature and salinity anomalies can explain 87% and 89% of the total variances, respectively. The first mode principle components of the temperature and salinity anomaly contain quasi-biennial periodicities. The salinity anomaly also contains an additional signal at a decadal timescale. Seasonal variations in the temperature and salinity are primarily associated with heat flux and freshwater discharge. However, the surface heat flux anomaly only accounts for 17% of the total variance of the time rate change of the temperature anomaly, and the freshwater discharge anomaly explains 25% of the variance of the salinity anomaly. Contrary to traditional paradigm about estuaries, this result shows that forcings other than local processes control the interannual variabilities of the temperature and salinity in LIS, most probably through horizontal exchanges. Also, the significant correlation between the salinity anomaly and the Gulf Stream (GS) position suggests that the interannual variability of salinity in LIS is possibly connected to shelf slope water properties associated with changes in the GS position.