Ocean-color remote sensing is routinely used to derive marine geophysical parameters from sensor-observed spectral water-leaving radiances. However, in clear geometrically shallow regions, traditional ocean-color algorithms can be confounded by light reflected from the seafloor. Such regions are typically referred to as "optically shallow". When performing spatiotemporal analyses of ocean color datasets, optically shallow features such as submerged sand banks and coral reefs can lead to unexpected regional biases. Most contemporary approaches mask or flag suspected optically shallow pixels based on ancillary bathymetric data. However, the extent to which seafloor reflectance contaminates the water-leaving radiance is dependent on bathymetry, water clarity and seafloor albedo. In this paper, an approach for flagging optically shallow pixels has been developed that considers all three of these variables. In the method, the optical depth of the water column at 547 nm, ζ(547), is predicted from bathymetric data and estimated water-column optical properties. If ζ(547) is less then the pre-defined threshold, a pixel is flagged as potentially optically shallow. Radiative transfer modeling was used to identify a conservative threshold value of ζ(547) = 20 for a bright sand seafloor. In addition, pixels in waters shallower than 5 m are also flagged. We also examined how varying bathymetric datasets may affect the optically shallow flag using MODIS data. It is anticipated that the optically shallow flag will benefit end-users when quality controlling derived ocean color products. Further, the flag may prove useful as a mechanism for switching between optically deep and shallow algorithms during ocean color processing.