Chlorophyll a is a green pigment found in plants. It absorbs sunlight and converts it to sugar during photosynthesis. Chlorophyll a concentrations are an indicator of phytoplankton abundance and biomass in coastal and estuarine waters. They can be an effective measure of trophic status , are potential indicators of maximum photosynthetic rate (P-max)  and are a commonly used measure of water quality. High levels often indicate poor water quality and low levels often suggest good conditions. However, elevated chlorophyll a concentrations are not necessarily a bad thing. It is the long-term persistence of elevated levels that is a problem. For this reason, annual median chlorophyll a concentrations in a waterway are an important indicator in State of the Environment .
It is natural for chlorophyll a levels to fluctuate over time. Chlorophyll a concentrations are often higher after rainfall, particularly if the rain has flushed nutrients into the water. Higher chlorophyll a levels are also common during the summer months when water temperatures and light levels.
Tidal regime is an important control on algal biomass (see Figure 2) . Strong tidal mixing lowers chlorophyll a concentrations because the residence time of algae in the photic zone is reduced . Tidal mixing also causes fine sediment to resuspend, and the elevated turbidity levels that result reduce the amount of light available for photosynthesis.
Changes to systems which decrease (e.g. construction of canal estates) or increase (e.g. breakwaters, training water and dredging) flushing rates influence chlorophyll a concentrations because flushing dilutes nutrients and moves them away from plants, making them less available. Conversely, slow moving or stagnant waters let nutrients increase and cell numbers grow.
Figure 1. Annual inorganic nitrogen loads vs. primary production for some marine and coastal waterways from around the world (from Nixon 1992 ; reproduced with permission of Scott Nixon). Data indicated by lime green dots are based on the work of Samantha Wellman (Ph.D in prep), and are reproduced with the permission of P. Scanes (NSW Department of Environment and conservation).
Phytoplankton productivity is one of the main forces regulating our planetary climate for via impacts on atmospheric carbon dioxide levels which are closely linked to the oceanic carbon dioxide concentrations . However, excessive water column productivity, expressed by high chlorophyll a concentrations, can supply large amounts of easily decomposition (i.e. labile) organic matter to the sediments. The decomposition of algal biomass can increase the diurnal amplitude of water column pH and dissolved oxygen fluctuations, and in some cases may lead to anoxic & hypoxic events. Moreover, elevated chlorophyll a levels indicate high numbers of phytoplankton and free floating macroalgae which can shade seagrass meadows leading to a decline in seagrass distribution . The above changes can translate into changes in animal and plant species diversity .
Nutrient impacts on coastal waterways (reflected in elevated chlorophyll a concentrations) depends on both the loads and bioavailability of nutrients, and the extent to which hydrodynamic features (e.g. residence times and mixing) and turbidity levels buffer nutrient loads .
Chlorophyll a concentrations are generally low in meso- and macro-tidal systems (e.g. deltas, estuaries and tidal creeks with mean tidal range >2m) due to the strong tidal flushing, and because tidal resuspension gives rise to high turbidity levels (discussed above) (Figure 2). By comparison, micro-tidal coastal waterways (e.g. wave-dominated estuaries, enclosed bays and shallow coastal lagoons with mean tidal range <2m) with limited river flushing can have quite high chlorophyll a concentrations and these concentrations have been shown to increase linearly with DIN at some international sites (see Figure 2). It is interesting that data from micro-tidal coastal waterways in New South Wales (NSW) do not fit the general linear trend of other micro-tidal waterways, but rather show a non-linear response at DIN concentrations <7 Ámol L-1 . A physiological explanation was forwarded for this discrepancy - that algal cells exposed to DIN at low to medium concentrations take up DIN in roughly linear proportions. However, at higher DIN concentrations, the cells capacity to take up DIN is saturated (see also ). The low nutrient status of NSW estuaries  combined with high uptake efficiencies  likely explains the observed pattern, and even the modest increases in chlorophyll reported here are indicative of moderate degradation ( additional information is also provided in the nutrients information sheet).
Figure 2. Annual average chlorophyll-a concentrations vs annual average dissolved inorganic nitrogen (DIN) concentrations for some non-Australian micro-tidal (tidal range <2 m) and macro-tidal estuaries (tidal range >2 m) (data from Monbet (1992) ) and some NSW micro-tidal estuaries (data from ). (Image reproduced with permission of K. Hinga  and P. Scanes (NSW Department of Environment & Conservation).
Phytoplankton assimilate available nutrients over their lifetime, whereas water column inorganic nutrient concentrations are notoriously variable over much shorter time scales .
Phytoplankton respond rapidly to pulsed nutrient inputs that might otherwise go undetected by regular nutrient sampling .
Chlorophyll a samples require minimal processing and storage in the field and are not easily contaminated .
Chlorophyll a is cheap in comparison to the analysis of a full suite of dissolved nutrients .
Remote sensing can detect chlorophyll concentrations but cannot detect nutrient concentrations such as phosphorous and nitrogen directly .
Phytoplankton populations can exhibit significant spatial and temporal variation (e.g. some algae migrate up and down within the water column) and concentrations can be quite different along lengths of the waterways or estuaries. The design of field studies needs to take this into account. However, surface chlorophyll a concentrations discussed below) can be estimated from satellite data, and can redress this gap in our understanding of the temporal and spatial variations of phytoplankton biomass
There is not always a clear relationship between chlorophyll concentration and biomass or cell number because of species differences in size and chlorophyll content .
Chlorophyll a is usually collected from water samples of a known volume that are filtered through fine mesh filter paper (0.45 micron) which is then analysed for chlorophyll a concentrations. There are three standard methods for determining chlorophyll a concentrations: spectrophotometry, fluorometry and high performance liquid chromatography (HPLC). Spectrophotometry is the most commonly used method, although the slower and more demanding HPLC method is able to differentiate between chlorophyll types and accessory pigments. Fluorometers transmit an excitation beam of light in the blue range (440 nm - 460 nm) and detect the light fluoresced by chlorophyll in a sample in the red wavelength (685 nm). This fluorescence is directly proportional to the concentration of chlorophyll. Although fluorescence is an indirect method for measuring chlorophyll a, field instrumentation allows this measurement to be made in situ and in a time-series.
Satellite remote sensing of chlorophyll concentrations rely on the absorption and scattering characteristics of phytoplankton and the way these optical properties affect the underwater light field and the reflectance (Rrs) or radiance (nLw) values measured by the satellite sensor . Information on chlorophyll a concentrations is obtained by using appropriate algorithms that relate measurements of remote sensing reflectance spectra either directly to chlorophyll concentration (empirical algorithms), or to optical properties of phytoplankton and other optically active materials in the water (semi-analytical algorithms, based on radiative transfer and theoretical relationships) (See Figure 3; ).
Figure 3. Map of the log-transformed chlorophyll values (log mean) for the dry season in Keppel Bay, Queensland, for the period May - December 2003 of the CHL retrieval by the MIM algorithm [from 14]
Various data sets can be found in state agencies, Commonwealth institutions and universities. Further details can be obtained on eutrophication and algal blooms from the National Eutrophication Management Program. The ANZECC/ARMCANZ Water Quality Guidelines  list default trigger values for chlorophyll a concentrations for coastal waterways in different geographic regions. The chlorophyll a threshold for impacts on fish is generally considered to be 100 micrograms of chlorophyll a per litre . the Department of Environment, Water, Heritage and the Arts provides guidelines for State of the Environment reporting . The relationships between chlorophyll a concentrations and nutrient loads in different types of coastal waterways can be explored using the Simple Estuarine Response Model developed by CSIRO.
More information on nutrients (changed from natural).
Vittorio Brando, CSIRO Land and Water
Andrew Moss, Queensland EPA
Lynda Radke, Geoscience Australia
David Rissik, NSW Land and Water Conservation
Tom Rose, Waters and Rivers Commission, Western Australia
Peter Scanes, Department of Environment and conservation, NSW
Samantha Wellman, School of Applied Sciences, University of Newcastle