Critical research questions such as how geomorphic and sedimentary systems modulate sediment movements and what are the timing, controls, and duration of significant sediment transport and deposition over submillennial to millennial timescales are still poorly understood, especially in the semi-arid Southern California. Although several sediment tracing and chronometric methods are available to address these questions, we still do not know well about the dominant controls and durations of sediment transport from the upper catchment source to the downstream sink. To examine this issue, here we used luminescence ages from K-feldspar sand grains from the range-front nested alluvial fans to the ~12-km-downstream in the flood plains of the Mission Creek catchment, Southern California. From a total of 29 sediment samples with >1,400 single grain (175–215 µm sizes) luminescence ages, we identified at least six depositional periods both in the upstream and downstream deposits in the catchment with no significant lag during the Holocene. Additional six significant depositional periods are also identified during the late Pleistocene (since the last ~100 ka) in the upstream alluvial fan deposits. These depositional periods correspond reasonably well with the late Pleistocene and Holocene intervals of wetter-than-average climate conditions based on hydroclimatic proxies from nearby locations. We, therefore, reinforces the concept that climate, especially wetter intervals, likely plays the first-order control on significant sediment deposition on submillennial to millennial timescales in the Mission Creek catchment. We also applied a detailed multi-elevated-temperature post-IR IRSL (MET-pIRIR) dating and bleaching experiment to examine whether sediment migration from the upstream to the downstream produces any significant changes in luminescence measurement (equivalent dose) signals. Any substantial changes in MET-pIRIR signals will be used to quantify the sediment movement characteristics (i.e., repeated flooding and burial events) within the catchment system.