Coastal stations are critical for interpretation of continental-scale CO2 exchanges although the impacts of land and sea breezes, local topography, katabatic winds, and CO2 transport from nearby terrestrial ecosystems are not well characterized. We applied a modeling framework that couples meteorological (MM5), land-surface (LSM1), and tracer models to investigate the impact of these factors on coastal CO2 measurements. Model predictions compared well with measurements over 4 months at our case study site (Trinidad Head, California). We predicted that during midday and under strong onshore wind conditions, positive and negative CO2 anomalies from the assumed “background” marine layer air were sampled at the station. These anomalies resulted from two classes of mechanisms that couple transport and recent terrestrial ecosystem exchanges. First, and most important, are local and large-scale recirculation of nighttime positive CO2 anomalies resulting from katabatic flows off the coastal mountain range. Second, negative anomalies generated by daytime net ecosystem uptake can be transported offshore in the residual layer and then entrained in the marine boundary layer. We predicted monthly averaged CO2 anomalies associated with terrestrial exchanges of 0.53, 0.34, 3.1, and 0.05 ppm during March, June, September, and December of 2002. Positive anomalies from nighttime ecosystem respiration were more likely to be sampled than are negative anomalies associated with daytime net ecosystem uptake. Current atmospheric models used in continental-scale inverse studies do not resolve these two classes of mechanisms and therefore may infer incorrect CO2 exchange rates.