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Bio-optical variability of surface waters in Northeastern Gulf of Mexico (NEGOM) was examined using satellite and in situ data. Relatively high chlorophyll-a concentration (chl>=1 mg m-3) and high colored dissolved organic mater (ag443>=0.1 m-1) were generally observed inshore, near major river mouths, and in plumes of Mississippi River water that extended offshore during the three consecutive summer seasons (1998, 1999, and 2000). River discharge dominated chlorophyll-a concentration variability inshore, particularly near major river mouths. Strong interannual variability in chlorophyll-a concentration was observed inshore from Escambia to Tampa Bay region during the winter to spring transition, which was different in 1998 compared to the winter to spring transition in 1999 and 2000. This was related to higher fresh water discharge during the 1997-1998 El Niño-Southern Oscillation event as well as strong upwelling in spring 1998. The Mississippi plume extended >500 km southeast of the Mississippi delta and up to the Florida Keys was observed for the periods extending over 14 weeks between May and September every year of the study. In general, ag443 covaried linearly and inversely with salinity inshore during spring and fall, indicating conservative mixing. The NEGOM salinity-ag443 relationship of fall 1998, i.e., Salinity=36.59-29.86*ag443 (n=8771, r2=0.86; 0.01<=ag443<=0.52, 16 <=S<=36), served as the best predictor of NEGOM salinity based on in situ ag443 observations for spring and fall seasons from all years (<3% mean percentage errors; corresponding to <1.03 psu). This may help estimate salinity from satellite ocean color data, but further testing using data from multiple years is needed to improve such relationship. While river discharge was an important source of colored dissolved organic matter (CDOM), phytoplankton blooms also contributed to CDOM formation in the NEGOM. Using a pigment index of phytoplankton taxonomic groups, the variability in biomass proportion of microphytoplankton explained up to 76% of the variability of the average of normalized phytoplankton absorption coefficients (545, 625, and 673 nm). The clorophyll-specific absorption coefficient, a*ph(440), varies by a factor of 7 (0.02-0.15 m2mg-1). Particle size and pigment composition played important roles in determining a*ph(440) variability. This must be accounted for in chlorophyll-a concentration algorithms based on aph.

The objective of this dissertation is to gain a better understanding of the environmental and climatic effects on the temporal and spatial variability of phytoplankton biomass along the West Florida Shelf. Chapter 1 examines temporal and spatial patterns in chlorophyll concentrations using satellite data collected between 1997 and 2003. Chlorophyll data derived from the SeaWiFS sensor are validated with in-situ data and analyzed. Wind, current, sea surface temperature, river, and rain data are used to better understand the factors responsible for the patterns observed in the satellite data. My question is whether the standard OC4 algorithm is adequate for studying short-term variability of chlorophyll concentrations along the WFS. I will examine temporal and spatial trends using the OC4 and compare them to the Carder semianalytical algorithm which uses remote sensing reflectances at 412nm, 443nm, 490nm,and 555nm to estimate chlorophyll concentrations separately from CDOM estimates. In Chapters 2 and 3 the potential problems due to CDOM and bottom reflectance are examined. In Chapter 2 I analyze the influence of riverine induced CDOM. Water leaving radiances are analyzed in an effort to discriminate true chlorophyll patterns from CDOM contaminated signals. Chapter 3 examines the impact of bottom reflectance on the satellite signal by using the percentage of remote sensing reflectance at a wavelength of 555 to differentiate between optically shallow waters and optically deep waters. Optically shallow waters are defined as those with the percentage of Rrs at 555 due to bottom reflectance greater than or equal to 25 percent, while optically deep waters have percent bottom reflectance less than or equal to 25 percent. These analyses will help assess the validity of the temporal and spatial patterns ofchlorophyll concentration observed with the SeaWiFS data described in Chapter 1.