Millions of people in the arid Southwest United States rely on snow-fed Colorado River water. Dust deposition on snow accelerates snowmelt, posing a challenge for water managers who also need to grapple with increased likelihood of drought due to climate change. Dust production is thought to increase during drought, but the impact of drought on dust deposition is unclear. To answer this question, total dust mass accumulation rate (DMAR) reconstructions were developed from sediment cores from three lakes in the San Juan Mountains, Colorado, spanning the last ~15,000 years. Monte-Carlo end-member analysis of particle size and elemental composition, which incorporates measurement and model uncertainties, was combined with age uncertainty to estimate DMAR for each lake. We also synthesize the records providing the first Holocene DMAR reconstruction for the region. The records show little relation between periods of frequent and severe drought (e.g. during medieval megadroughts) and periods of higher DMAR, although there is considerable uncertainty at short timescales. We find instead that sediment availability, modulated by natural or human-mediated geomorphic processes that generate sediment, and transport mechanisms are the key drivers. DMAR was highest during the Late Glacial-Interglacial Transition (LGIT, 15–11 kyr BP) and in the last 250 years, periods when sediment availability was enhanced. DMAR increased by 60% (16–85% 75% highest density region range) compared with the late-Holocene baseline starting in the 1770s and peaking in the 1840s, associated with the intensification of human activities. Human-induced dustiness also represents the highest interval of dust deposition in the last 11,000 years. Our results demonstrate that although the Colorado Plateau is naturally prone to dustiness, drought is a secondary driver of dust accumulation in the mountains. This suggests that land-use management decisions aimed at reducing land disturbance can mitigate future dust accumulation, despite projected increases in regional aridity.