Sediment deposited within lake basins can preserve detailed records of past environmental conditions on planetary surfaces, including both Earth and Mars. Establishing how to best characterize these paleoclimate records is thus critical for understanding the evolution of past planetary climates. Here, we present an ∼40 k.y. lake sediment record from Lake Towuti, Indonesia, developed using visible to near-infrared (VNIR) reflectance spectroscopy. Source sediment from the main river input to Lake Towuti, the Mahalona River, is spectrally dominated by Mg-rich serpentine; however, we also identify a distinct Al-phyllosilicate component, which we interpret as kaolinite, that increases in relative proportion to serpentine with decreasing grain size. Sink sediment from two cores collected at the distal margins of the Mahalona River delta has similar spectral signatures to the input source sediment. The cores capture systematic variations in the proportion of Al-phyllosilicate to serpentine over time, which is also expressed in changes in bulk elemental chemistry of the sediment. We show that the abundance of serpentine relative to Al-phyllosilicate increases dramatically during the globally cooler, regionally drier climate of the Last Glacial Maximum. This change records the grain size–dependent mineralogy of deltaic sediment, which is ultimately driven by forced delta progradation and river incision during lake lowstands. Our analyses show that VNIR reflectance spectroscopy offers a rapid, nondestructive, and effective method for developing paleoenvironmental records from sedimentary phyllosilicate mineralogy. Exposed paleolake deposits on Mars should preserve similar paleoenvironmental information that can be accessed through detailed remote sensing observations of stratigraphy and VNIR reflectance spectroscopy in a source-to-sink framework.