Water Quality CTD Profiles and Grab Samples 
Profiles of water quality parameters were measured using the Seabird SBE 19 CTD with 
data logging capability. Variables measured by the CTD and other associated instrumentation 
are depth, temperature, conductivity, turbidity, photosynthetically active radiation (PAR), and in 
situ fluorescence, and calculated variables include salinity and density. During 2006 cruises, 
dissolved oxygen was measured at discrete depths. Discrete water samples were collected at 
representative depths (surface, mid-depth, and bottom) for analysis of chlorophyll a , total 
suspended solids, and dissolved inorganic nutrients. Since this report includes data collected for 
various projects and principal investigators, the number and location of discrete samples varied 
with sampling interval. 
For each water quality profile, the CTD was lowered to the bottom, and discrete water 
samples were collected during the upcast at bottom, mid-depth and surface depths. Near-bottom 
conditions were measured at 0.5 m above the bottom. Data were collected every second and 
binned with ‘Seasoff software into 0.25 m discrete intervals. During 2006 cruises, dissolved 
oxygen was collected using a YSI 6600 Sonde attached to the CTD cage. The YSI sonde was 
calibrated prior to use following the manufacturer’s specifications. Light attenuation coefficients 
(, k ) were calculated for the water column on the downcast. Prior to analysis the data were 
reviewed to eliminate any false reading caused by reflection from the aluminum boat. Care was 
taken so that the PAR sensor on the CTD was not in the shadow of the boat. 
The water column was sampled at each site for dissolved inorganic nutrients (Si(OH) 4 , 
NO 3 +N0 2 , NH 4 , and P0 4 3 ), total nitrogen and phosphorous (2006 cruises only), chlorophyll a 
concentration, and total suspended solids (TSS). Water column samples were collected and 
prepared per MES SOP09.rev 0 (2003). Water quality samples were filtered and processed on 
board the boat or upon return to the laboratory within several hours of collection. 
A performance-based approach was used for evaluating the quality of the chemical 
analysis. Depending upon the compound, laboratory practices included 1) continuous laboratory 
evaluation through the use of Certified Reference Materials (CRMs) and/or Laboratory Control 
Materials (LCMs), 2) laboratory spiked sample matrices, 3) laboratory reagent blanks, 4) 
calibration standards, and 5) laboratory and field replicates. 
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