In this paper, we examine observations of shallow, stable boundary layers in the cool waters of the Gulf of Maine between Cape Cod, Massachusetts, and Nova Scotia, obtained in the 2004 New England Air Quality Study (NEAQS-04), which was part of the International Consortium for Atmospheric Research into Transport and Transformation (ICARTT). The observations described herein were made from the NOAA Research Vessel Ronald H. Brown. The ship was instrumented for measurements of meteorological, gas-phase and aerosol atmospheric chemistry variables. Meteorological instrumentation included a Doppler lidar, a radar wind profiler, rawinsonde equipment, and a surface flux package. In this study, we focus on direct comparisons of the NEAQS-04 flux observations with the COARE bulk flux algorithm to investigate possible coastal influences on air-sea interactions. We found significant suppression of the transfer coefficients for momentum, sensible heat, and latent heat; the suppression was correlated with lighter winds, more stable surface layers, S-SE wind direction, and lower boundary layer heights. Analysis of the details shows the suppression is not a measurement, stability correction, or surface wave effect. The correlation with boundary layer height is consistent with an interpretation that our measurements at 18-m height do not realize the full surface flux in shallow boundary layers. We also find that a bulk Richardson number threshold of 0.1 gives a better estimate of boundary layer height than 0.25 or 0.5. Mean ozone deposition velocity is estimated as 0.44 mm s−1, corresponding to a boundary removal timescale of about 1 day.