A drifter equipped with bio-optical sensors and an automated water sampler was deployed in the California Current as part of the coastal transition zone program to study the biological, chemical, and physical dynamics of the meandering filaments. During deployments in 1987 and 1988, measurements were made of fluorescence, downwelling irradiance, upwelling radiance, and beam attenuation using several bio-optical sensors. Samples were collected by and automated sampler for later analysis of nutrients and phytoplankton species composition. Large-scale spatial and temporal changes in the bio-optical and biological properties of the region were driven by changes in phytoplankton species composition which, in turn, were associated with the meandering circulation. Variance spectra of the bio-optical parameters revealed fluctuations on both diel and semiurnal scales, perhaps associated with solar variations and internal tides, respectively. Offshore, inertial-scale fluctuations were apparent in the variance spectra of temperature, fluorescence, and beam attenuation. Although calibrations samples can help remove some of these variations, these results suggest that the use of bio-optical data from unattended platforms such as moorings and drifters must be analyzed carefully. Characterizations of the scales of phytoplankton variability must account for the scales of variability in the algorithms used to convert bio-optical measurements into biological quantities.