In recent years, California has been suffering from severe hydroclimatic related challenges, such as droughts, fires, and deluges. Despite many ongoing efforts, uncertainties remain regarding the natural variability of hydroclimatic system and how anthropogenic impacts will affect future climate dynamics. To better understand the issues, it is essential to understand paleo-hydroclimatic variability over the long-term during the period that human beings had little impact on the climate. This dissertation aims to investigate long-term centennial to millennial hydroclimatic changes to understand natural variability to help differentiate this from anthropogenic impacts on the current climate and to plan for future climate change (e.g. formulating relevant policies, proposing contingency plans, etc.). Lake sediments preserve long hydroclimate records useful for resolving long-term variability.Among the feasible proxy indicators used to reconstruct paleo-hydroclimate, I utilized diatom microfossils (microscopic algae) because they have been shown to record lake level and salinity changes within lakes that reflect changes in precipitation and evaporation. I analyzed the fossil and modern diatom flora from Kelly Lake in Northern California and from Baldwin Lake in Southern California. This dissertation focuses on the late Quaternary overall while focusing specifically on the Holocene changes in Northern California and Pleistocene changes in Southern California. From Kelly Lake, I established diatom-inferred water depth transfer functions to quantitatively infer the past lake level changes during the Holocene. The results show a meaningful correlation between modern diatom assemblages and water depths, allowing the construction of statistical transfer functions with high R2 values (>0.95). This is the first such single-lake transfer function developed in California and one of only a handful worldwide. The transfer functions are then applied to the fossil diatom flora from a Holocene-length sediment core from Kelly Lake. The quantitatively reconstructed lake level changes in Kelly Lake indicate appreciable variations over the Holocene and suggest the influences from global drivers such as solar radiative and El Ni�o-Southern Oscillation forcings to the hydroclimatic variability in the Northern Coast Ranges. In Southern California, the qualitatively inferred salinity and water depth changes in Baldwin Lake showed abrupt change at about 70,000 cal yr BP when the orbitally controlled radiative forcing transitioned high seasonal variability to low seasonal variability. In both Northern and Southern California, the diatom records indicate a high degree of sensitivity by hydroclimate to external drivers related to external forcing factors such as ocean conditions and orbital variations.