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In the California Current system (CCS), coherent structures such as jets and eddies strongly control the biological response to coastal upwelling. One of the outstanding problems in marine ecology is to understand the mechanisms of larval transport. Details of transport dynamics from nearshore to offshore, and subsequent delivery of coastally spawned propagules back to favorable settlement areas, strongly control marine population dynamics. Recent developments in applied dynamical systems allow the identification of coherent structure boundaries by numerical calculation of Lagrangian coherent structures (LCS), finite-time analogs of stable and unstable manifolds of hyperbolic fixed points. These material lines divide the flow into regions of disparate transport fate and illuminate the skeleton of filamentation and mixing. Using altimetric observations of the CCS, we show that LCS are less sensitive to noise and under-resolution than Eulerian metrics, and can map events undetectable by analysis of the frozen-time velocity field. However, small-scale dynamics such as lobes are not well resolved by altimetric observations. In an ocean circulation model of an idealized CCS, LCS are used to track filamentation and eddy-eddy interactions, important larval transport pathways from the shelf offshore. Filaments and packets caused by eddy-eddy interaction are stable to horizontal swimming perturbations, as predicted by the structural stability of hyperbolic manifolds. Retention in the upwelling jet is high and strongly patterns larval settlement. Settlement events are best correlated with integrated upwelling intensity and not upwelling relaxation events as commonly assumed. These studies demonstrate that coherent structures play a large role in coastal ecosystems, and that techniques and theorems from dynamical systems can provide insight into dominant transport pathways controlling coastal ecosystems.