The past 12 years have seen significant steps forward in the science and practice of coastal flood analysis. This paper aims to recount and critically assess these advances, while helping identify next steps for the field. This paper then focuses on a key problem, connecting the probabilistic characterization of flood hazards to their physical mechanisms. Our investigation into the effects of natural structure on the probabilities of storm surges shows that several different types of spatial-, temporal-, and process-related organizations affect key assumptions made in many of the methods used to estimate these probabilities. Following a brief introduction to general historical methods, we analyze the two joint probability methods used in most tropical cyclone hazard and risk studies today: the surface response function and Bayesian quadrature. A major difference between these two methods is that the response function creates continuous surfaces, which can be interpolated or extrapolated on a fine scale if necessary, and the Bayesian quadrature optimizes a set of probability masses, which cannot be directly interpolated or extrapolated. Several examples are given here showing significant impacts related to natural structure that should not be neglected in hazard and risk assessment for tropical cyclones including: (1) differences between omnidirectional sampling and directional-dependent sampling of storms in near coastal areas; (2) the impact of surge probability discontinuities on the treatment of epistemic uncertainty; (3) the ability to reduce aleatory uncertainty when sampling over larger spatial domains; and (4) the need to quantify trade-offs between aleatory and epistemic uncertainties in long-term stochastic sampling.