We are attempting to simulate the transport of pollutants from through air and water pathways in an urban environment by linking cross-disciplinary subsystem models, tailoring them for urban applications, and writing interface physics modules. We are focusing on the transport and fate of nitrates because 1) they track through both the air and water pathways, 2) the physics, chemistry, and biology of the complete cycle is not well understood, and 3) nitrates have important health, local ecosystem, and global climate implications. We are currently simulating the fate of nitrates in the Los Angeles basin from their beginning as nitrate-precursors produced by auto emissions and industrial processes, tracking their dispersion and chemistry as they are transported by regional winds and eventually wet or dry deposit on the ground, tracing their path as they are entrained into surface water runoff during rain events and then carried into the stormwater system where dispersion and biologically-mediated chemical reactions take place. We wish to give an overview of the project and show our current work-to-date involving the linking together of mesoscale atmospheric, air pollution chemistry and deposition, and urban stormwater transport, chemistry, and biology models.