Light attenuation is a critical parameter governing the ecological function of shallow estuaries. In these systems primary production is often dominated by benthic macroalgae and seagrass; thus light penetration to the bed is of primary importance. We quantified light attenuation in three seagrass meadows in Barnegat Bay, New Jersey, a shallow eutrophic back-barrier estuary; two of the sites were located within designated Ecologically Sensitive Areas (ESAs). We sequentially deployed instrumentation measuring photosynthetically active radiation, chlorophyll a (chl a) fluorescence, dissolved organic matter fluorescence (fDOM; a proxy for colored dissolved organic matter (CDOM) absorbance), turbidity, pressure, and water velocity at 10 min intervals over 3-week periods at each site. At the southernmost site, where sediment availability was highest, light attenuation was highest and dominated by turbidity and to a lesser extent chl a and CDOM. At the central site, chl a dominated followed by turbidity and CDOM, and at the northernmost site turbidity and CDOM contributed equally to light attenuation. At a given site, the temporal variability of light attenuation exceeded the difference in median light attenuation between the three sites. Vessel wakes, anecdotally implicated in increasing sediment resuspension, did not contribute to local resuspension within the seagrass beds, though frequent vessel wakes were observed in the channels. With regards to light attenuation and water clarity, physical and biogeochemical variables appear to outweigh any regulation of boat traffic within the ESAs.