Lagrangian Coherent Structures (LCS), as the time-varying analogs of stable and unstable manifolds of hyperbolic fixed points, are used to identify flow transport boundaries and cores of filamentation. An increasing number of studies highlight the importance of these flow structures in organizing biological responses in mesoscale oceanography. Here I introduce the theory, numerical detection, sensitivity to errors, and application of LCS in the California Current System using two data sets: velocity fields from satellite altimetry and ocean model output. Sensitivity of LCS are examined in the altimetry fields, and found to be extremely robust to undersampling and interpolation error. LCS are then applied to the problem of coastal larval transport in upwelling systems, where filamentation, marked by attracting LCS, dominates offshore transport and drives patchiness production, creating dense packets that survive strong perturbation, including particle behavior.