Marked uncertainties persist regarding the climatic evolution of the Mediterranean region during the Holocene. For instance, whether moisture availability gradually decreased, remained relatively constant, or increased during the last 7000 years remains a matter of debate. To assess Holocene limnology, hydrology and moisture dynamics, the coastal lakes Lago Preola and Gorgo Basso, located in southwestern Sicily, were investigated through several stratigraphic analyses of ostracodes, including multivariate analyses of assemblages, transfer functions of salinity, and biochemical analyses of valves (Sr/Ca, δ18O and δ13C). During the early Holocene, the Gorgo Basso and Lago Preola ostracode records are similar. After an initial period of moderate salinity (1690–6100 mg/l from ca. 10,000–8190 cal yr BP), syndepositional or diagenetic dissolution of ostracode valves suggests that salinity declined to <250 mg/L from ca. 8190 to 7000 cal yr BP at both sites. After ca. 6250 cal yr BP, the ostracode records are strikingly different. Lago Preola became much more saline, with paleosalinity values that ranged from 2270 to about 24,420 mg/L. We suggest that Lago Preola's change from a freshwater to mesosaline lake at about 6250 cal yr BP was related to sea level rise and resulting intrusion of seawater-influenced groundwater. In contrast, Gorgo Basso remained a freshwater lake. The salinity of Gorgo Basso declined somewhat after 6250 cal yr BP, in comparison to the early Holocene, ranging from about 550 to 1680 mg/L. Cypria ophtalmica, a species capable of rapid swimming and flourishing in waters with low dissolved oxygen levels, became dominant at approximately the time when Greek civilization took root in Sicily (2600 cal yr BP), and it completely dominates the record during Roman occupation (roughly 2100 to 1700 cal yr BP). These freshwater conditions at Gorgo Basso suggest high effective moisture when evergreen olive-oak forests collapsed in response to increased Greco-Roman land use and fire. Ostracode valve geochemistry (Sr/Ca, δ18O) suggests significant changes in early vs. late Holocene hydrochemistry, either as changes in salinity or in the seasonality of precipitation. Harmonizing the autecological and geochemical data from Gorgo Basso suggests the latter was more likely, with relatively more late Holocene precipitation falling during the spring, summer, and fall, than winter compared to the early Holocene. Our ostracode-inferred paleosalinity data indicate that moisture availability did not decline during the late Holocene in the central Mediterranean region. Instead, moisture availability was lowest during the early Holocene, and most abundant during the late Holocene.