This study analyzes the hydrological variability in Bahia de La Paz, the largest bay in the Gulf of California. The hydrographic data were obtained in different seasons between 1995 and 2005. A persistent spatial and seasonal variability in temperature and salinity occurred in the bay during the study. In springs and summers, an absence of a mixed layer and the presence of a sharp thermocline were observed, while in autumns and winters the presence of a mixed layer and a less intense thermocline was noticeable. There was not a defined pattern in relation to the salinity variation because this depended on the water masses present in the region. In fact, when Equatorial Surface Water intruded into the bay, a considerable salinity decrease was recorded which originated the absence of the halocline, as observed during El Niño 1997-1998. El Niño event produced warming waters in the entire column of the bay, having its stronger effects during summer 1997, with a temperature increment of 2°C. Stratification in the bay depends on the water masses present but not on the seasons of the year.