Abstract. The use of new autonomous and Lagrangian platforms (e.g. gliders, drifters, etc.) has revolutionized sampling of the ocean. The incorporation of in vivo chlorophyll-a fluorometers into these platforms for characterizing chlorophyll-a concentrations and phytoplankton biomass has reinforced the need for a thorough understanding of the variability and biases associated with basic fluorescence measurements. Seaglider, a long-range autonomous glider, has been deployed routinely in Northeast Pacific waters off the Washington coast, USA. Measurements of chlorophyll-a fluorescence (proxy for chlorophyll-a concentration) and optical backscattering (proxy for particle concentration) were collected on the continental shelf and along a V-shaped transect that extended 200 km from the continental shelf into deep oceanic waters. Daytime fluorescence quenching (i.e. the reduction in the fluorescence quantum yield often observed during daylight hours) could be detected throughout the dataset, with near-surface daytime fluorescence quenched by as much as 80% during summer. Quenching was observed throughout the region, at all times of year, and to depths greater than 50 m. The degree of quenching was positively correlated with incoming solar radiation and the observed pattern was remarkably similar to what has been observed in other areas, suggesting some degree of universality for the underlying relationship.

From September 2003 to December 2007, autonomous, underwater Seaglider continuously ran a V-shaped transect off Washington State from about 200-m water depth (i.e., at the break between the shelf and slope) to offshore waters with depths .2700 m. Seaglider visited the offshore vertex at 47uN, 128uW, where our observations concentrated, approximately monthly. Seaglider measured temperature, conductivity, and dissolved oxygen to 1000 m and also recorded chlorophyll a (Chl a) fluorescence and particulate optical backscatter to 150 m. Distinct interannual variation was documented in timing and depths of winter mixing, transition to a shallow summer pycnocline, and onset of mixed-layer erosion in autumn. Chl a concentrations estimated from fluorescence were directly comparable among the seven laboratory-calibrated sensors used, but their estimates exceeded concurrent, satellite-derived concentrations by a factor of three. Seaglider optical profiles enabled interpretation of satellite imagery by revealing that the apparent autumn bloom after destratification was instead a vertical redistribution of phytoplankton from the subsurface maximum to a depth where they could be observed by satellites. Results of 4 yr of sampling within 25 km of the vertex demonstrate the value of gliders in ocean observing and their capability to carry out multiyear, fully autonomous operations under any sea state. The true power of glider programs will be realized in combination with other measurement platforms, including larger spatial coverage by satellites and more comprehensive biogeochemical measurements from moorings and occasional ship-based sampling.

Nutrient pollution from rivers, nonpoint source runoff, and nearly 100 wastewater discharges is a potential threat to the ecological health of Puget Sound with evidence of hypoxia in some basins. However, the relative contributions of loads entering Puget Sound from natural and anthropogenic sources, and the effects of exchange flow from the Pacific Ocean are not well understood. Development of a quantitative model of Puget Sound is thus presented to help improve our understanding of the annual biogeochemical cycles in this system using the unstructured grid FiniteVolume Coastal Ocean Model framework and the Integrated Compartment Model (CE-QUAL-ICM) water quality kinetics. Results based on 2006 data show that phytoplankton growth and die-off, succession between two species of algae, nutrient dynamics, and dissolved oxygen in Puget Sound are strongly tied to seasonal variation of temperature, solar radiation, and the annual exchange and flushing induced by upwelled Pacific Ocean waters. Concentrations in the mixed outflow surface layer occupying approximately 5-20 m of the upper water column show strong effects of eutrophication from natural and anthropogenic sources, spring and summer algae blooms, accompanied by depleted nutrients but high dissolved oxygen levels. The bottom layer reflects dissolved oxygen and nutrient concentrations of upwelled Pacific Ocean water modulated by mixing with biologically active surface outflow in the Strait of Juan de Fuca prior to entering Puget Sound over the Admiralty Inlet. The effect of reflux mixing at the Admiralty Inlet sill resulting in lower nutrient and higher dissolved oxygen levels in bottom waters of Puget Sound than the incoming upwelled Pacific Ocean water is reproduced. By late winter, with the reduction in algal activity, water column constituents of interest, were renewed and the system appeared to reset with cooler temperature, higher nutrient, and higher dissolved oxygen waters from the Pacific Ocean.

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