Pore water samples were extracted from the sediment using a battery-powered perstaltic pump. An amount in excess of the dead volume in the tubing that connected the well point to the pump (~270ml) was collected and discarded before taking each 250 ml pore water sample to ensure a pure pore water sample. The mixing of pore water during its passage through the tubing acted to homogenize the samples; however, samples collected from individual well points on and after 1 March 1997 were homogenized in a glass flask free of any head space to ensure uniformity between subsamples intended for different chemical analyses. There did not appear to be any significant change in the relative distribution of pore water species once this deliberate homogenization step was employed. An additional experiment was performed to determine how much pore water composition would change with the volume of water extracted. Four 60 ml pore water samples were sequentially taken from 7-, 25-, and 50-cm well points at each station using 60 ml syringes attached directly to the well points (without using the pump and tubing). These samples showed that nitrate and ammonium concentrations did not change significantly with the amount of pore water extracted, even for the 7-cm well points, suggesting that there was no enhanced movement of pore water along the sides of the well points.
Two arrays ~1.5 m apart were installed at varying distances from the forereef (Stations S and C) and sampled over a 9-month period. At no point was there a freshwater flow into the bay large enouch to effect surface salinities over the reef. Samples for the determination of dissolved nitrate, nitrite, and ammonium were filtered through glass fiber filters and analysed using standard colorometric techniques. Dissolved oxygen was measured in the field using an Orion model 820 dissolved oxygen meter equipped with a Clark-type electrode. Pore water nitrous oxide concentrations were measured following the method of Pierotti and Rasmussen (1980) with only minor modifications.
Sediment hydraulic conductivity was estimated for each of the well points using a falling-head permeameter. These estimates assumed that the sediments were homogeneous and extended infinitely around a given well point. These assumptions were made to simplify the required calculations; however, the sensitivity of the calculations to these assumptions at distances greater than 7 cm away from the well point was very small ( less than 5%).
#INSTRUMENT TYPES: Wells: 1/8 in. diameter schedule 80 PVC pipe
Water extraction: battery-powered perstaltic pump and 60 ml syringes
Dissolved oxygen was measured in the field using an Orion model 820 dissolved oxygen meter equipped with a Clark-type electrode.