The distribution and movement of chloropigments (chlorophylls and associated degradation products) in the bottom boundary layer near Duck, North Carolina, were examined during July and August 1994. Times series of chloropigment fluorescence, current velocity, and surface wave properties were acquired from instruments mounted on a bottom tripod set at 20 m depth. These data were combined with moored current meter measurements, meteorological data, and shipboard surveys in a comparative assessment of physical processes and chloropigment distribution over a wide range of temporal and spatial scales. Two dominant scales of chloropigment variation were observed. On numerous occasions, small-scale (order m) structure in the near-bottom fluorescence field was observed, even in the absence of identifiable structure in the temperature and salinity fields. Over larger time-scales and space scales, variations in fluorescence were related to changes in water mass properties that could be attributed to alternating events of upwelling and downwelling. This view was reinforced by shipboard measurements that revealed correlations between fluorescence and hydrographic fields, both of which were modified by wind-forced upwelling and downwelling and by the advection of low-salinity water from Chesapeake Bay. Local resuspension of sediments did not contribute appreciably to the near-bottom pigment load seen at the tripod, because of low bottom stress. Estimates of chloropigment flux indicated a net shoreward transport of chloropigments in the lower boundary layer. However, the rapid fluctuations of currents and pigment concentrations gave rise to large and frequent variations in chloropigment fluxes, generating uncertainty in extrapolations of this finding to longer timescales. ¿ 2001 American Geophysical Union