ABSTRACT Lacustrine basins and the sediments in them provide a critical component of regional tectonic development and climate history. Each sub-basin in the landscape records the interplay between active tectonism and shifting climate. Many of the basins in southern Nevada that contain deposits of the Muddy Creek Formation were closed fluvio-lacustrine systems during the latest Miocene and into the Pliocene. They were subsequently integrated into the regional Colorado River system. Lacustrine deposits of the Muddy Creek Formation are exposed along the trace of the Las Vegas Valley shear zone in the Nellis Dunes Recreation Area (NDRA), northeast of Las Vegas, Nevada. The Muddy Creek Formation in NDRA consists of approximately 130 m of mixed carbonates and clastics, and new tephrochronology suggests an early to late Pliocene age (∼ 4.7 to ∼ 2.6 Ma) for the lowermost lacustrine deposits and an unknown, but younger, age for the uppermost spring-fed lacustrine deposit. These sediments were deposited in an arid to semiarid lake (Lake Nellis) and alluvial floodplain system based on the interpretation of lithologies and facies associations. The stratigraphic succession coarsens upward and reflects establishment of a lacustrine carbonate system overlain by a clastic succession of peripheral lake sediments of alluvial and floodplain origin. The peripheral lake deposits consist of spring-fed and fluvial wetland mudflats of brown claystone and siltstone. This brown claystone is capped by a succession of yellow and red sandstones deposited by fluvial and minor eolian processes. The second, and youngest, freshwater limestone, likely disconformably, overlies the yellow and red sandstones, and is thought to be temporally and depositionally distinct from the underlying Muddy Creek deposits. The transition from the lower lacustrine carbonates to clastic fluvial channel and flood-plain deposits indicates desiccation of Lake Nellis and possibly occurs soon after ∼ 2.7 to ∼ 2.6 Ma based on the ages of tuffs occurring in the uppermost limestone and marl beds. This is consistent with an interpreted increase in regional aridity after ∼ 2.8 Ma (Smith et al. 1993). The second limestone deposit at the top of the section represents an even younger spring-fed lacustrine deposit of unknown age. Throughout the lower carbonate section, three tuffs were identified, and geochemically correlated, using a discriminant-function analysis, to the tuff of Napa (≤ 4.70 ± 0.03 Ma), the Putah Tuff (∼ 3.3 Ma), and the lower tuffs of the Badlands (∼ 2.7 to ∼ 2.6 Ma). The timing of deposition of Lake Nellis sediments postdates the integration of the three major lake systems in this region (Lake Grand Wash, Lake Hualapai, and Lake Las Vegas) into the Colorado River drainage (5.6–4.9 Ma), and also postdates the full integration of the river to sea level (4.8–4.63 Ma) (Howard et al. 2015; Crow et al. 2021). Lake Nellis represents an isolated lake basin that was one, and maybe the last, lacustrine system to be fully integrated into the Colorado River drainage in this region.