A literature review revealed a lack of data on primary productivity in New Zealand Estuarine waters. Water samples were collected and analysed for spectral absorption properties from a tidal salt-marsh mangrove lagoon over a period of seven months in a region of the Tamaki Estuary, Auckland, New Zealand. Samples were collected to determine primary productivity, to determine if the lagoon was an importer or exporter of nutrients in the form of chlorophyll a, and to compare change in pigment community structure, by spectral curve analysis, over various tidal regimes and temporal scales.

Chlorophyll a was routinely monitored by visible spectrophotometry at 665nm. Routine samples were collected at a single site, just after dawn and just prior to dusk at two hourly intervals, over a period of at least three consecutive days per month (July 2004–January 2005) and analysed by spectrophotometer with methanol as the solvent. Further samples were collected on a rapid transect in the adjacent Tamaki Estuary, from outer harbour to inner estuary to compare spectral properties and average abundance of chlorophyll (February 2005). A novel mathematical model for prediction of ratios of chlorophyll to pheophytin (at 665nm) is proposed, calculated on pre- and post-acidified spectrophotometric-determined laboratory data. A faunal survey was conducted in both winter and summer (October 2004 and February 2005) to provide baseline data on benthic biodiversity in the lagoon.

Analysis of variance determined significant differences for average absorbance at 665nm for water samples between hours, days and months of collection. No significant difference was recorded for average abundance at 665nm, for incoming or outgoing samples (import or export) either monthly or over the entire samples period. Average absorption increased from winter to spring, with detritus and products of chlorophyll degradation dominating the spectra during all routine sample periods (July 2004–January 2005). Significant peaks in absorbance were recorded during periods of elevated rain and wind activity, particularly when intertidal mudflat areas were exposed and when wind-generated wave action resuspended benthic sediments causing the development of a turbid fringe. Significant variation in chlorophyll abundance was recorded from outer to inner estuary in the February transect, as was change in spectral curve. In the outer estuary absorbance in the blue region peaked at ~ 410nm indicating the presence of detritus and chlorophyll degradation products. In the inner estuary the dominant peak in the blue region peaked at ~435nm indicative of the presence of water-bourne microalgae. This observation is supported by investigation of chlorophyll to pheophytin ratios, pre- and post-acidification.

Mathematical modelling provides extremely good agreement with laboratory-determined abundance for ratios of chlorophyll to pheophytin (R2 = 0.97). Macrofaunal biodiversity was not considered unusual for an urban catchment; the most abundant species present being Amphibola crenata, grazing upon muddy intertidal mudflats.

The results obtained from this study provide a preliminary record of spectral absorption properties for New Zealand estuarine waters, identifying detritus and products of chlorophyll degradation as dominating spectral absorption in Tahuna Torea estuarine water samples over the study period. No significant difference was detected for average absorbance incoming vs. outgoing water samples (import or export) from the lagoon. The methodologies used in this study may be applicable elsewhere.