Hazards due to the fundamental process of advection of natural and anthropogenic material in environmental flows are ubiquitous and profoundly impact society; preparedness and effective response can save many lives, untold environmental damage and enormous financial cost. Recent catastrophic examples include: oil spill advection during the Deep Water Horizon disaster, the passage of the ash cloud from the Eyjafjallajökull volcano through commercial air space, and the trail of radioactive waste from the Fukushima reactor disaster. On a day-to-day operational level, search-and-rescue operations at sea rely critically on correctly modeling and interpreting flow transport in order to inform life-or-death decisions. Understanding how flow transport is organized and predicting where things go in complex environmental flows remains a formidable scientific challenge, however, due to unsteady nonlinear and multiscale flows, ambiguities in defining material transport, multiple sources of uncertainty, the difficulty of identifying and acquiring pertinent data to assimilate into models, the variability of predictions across different models, and the complexity of analyzing vast data sets and visually representing the results. The NSF-ALPHA (Advanced Lagrangian Predictions for Hazards Assessments) team (MIT, WHOI, Virginia Tech and UC Berkeley) proposes transformational progress in tackling these science issues by exploiting and advancing recent fundamental breakthroughs in four-dimensional (3D plus time) Lagrangian methods. An integrated theoretical, computational and observational approach will be employed to develop, implement and utilize these cutting-edge Lagrangian methods with data-driven modeling for the purpose of uncovering, quantifying and predicting key transport processes and structures during regional flow-based hazards in the ocean and atmosphere. The challenges are broad in scope, encompassing engineering, geosciences, applied mathematics, and computational and information science and engineering. The overall goal of the ALPHA project is to employ an integrated theoretical, computational and observational approach to develop, implement and utilize these cutting-edge Lagrangian methods with data-driven modeling for the purpose of uncovering, quantifying and predicting key transport processes and four-dimensional (3D plus time) structures during regional flow-based hazards in the ocean and atmosphere.