The effect of tidal wetlands on dissolved organic carbon (DOC) concentrations and the chemical composition (quality) of DOC in the Sacramento-San Joaquin Delta waters is not well understood. Quantifying DOC fluxes into and out of tidal wetlands is important because DOC can adversely affect drinking water quality by contributing disinfection byproduct precursors, (DBPP). Here we report the results of a study to measure fluxes and chemical composition of wetland-derived DOC from Brown's Island, a natural tidal wetland in the western Delta. Measuring biogeochemical variables in estuarine environments on scales at which they are forced is impractical using traditional grab sampling and laboratory-based analysis. To better accomplish this, we implemented an in-situ hydro-optical instrumentation system capable of high frequency measurement of velocity using an acoustic doppler current profiler (ADCP) as well as a variety of biogeochemical proxies (absorbance, fluorescence) allowing the estimation of DOC fluxes on temporal scales of minutes over spring neap tidal cycles in the main sloughs of Brown's Island. Regression of the in situ optical data to traditional laboratory analyses of DOC quality and quantity in grab samples provides calibration for the use of optical parameters as proxies. The high resolution in-situ optical measurements paired with ADCP discharge measurements allowed us to compute the horizontal DOC flux into and out of the tidal wetland to help estimate the role of Delta wetlands in the transport and transformation of DOC on scales ranging from hours to weeks. Additionally, these measurements permit computations of the net tidal residual fluxes between the tidal wetland and the surrounding estuary. The magnitude of these fluxes varies on diurnal, weekly, and seasonal timescales in response to regional and local conditions. The results of the flux calculations will be presented with a discussion of their implications for wetland restoration in the western Delta.Downing, B., J. Fleck, M. Lionberger, N. Ganju, E. Boss, D. Schoellhamer, and B. Bergamaschi, 2006. An In-situ Hydro-Optical Sampling System to Measure Seasonal Changes in DOC Character and Fluxes from a Tidal Wetland. Ocean Optics Conference 2006, Montreal, Quebec.