The Cairns region is on the wet tropical coast of northeastern Queensland. It includes several major catchments and river systems. Agricultural (e.g. grazing, forestry and cropping) and urban developments are the primary land uses in coastal catchments and contribute high loads of nutrients and sediments to nearshore coastal waters.
Thirteen seagrass species have been recognised for this region. The most extensive areas of seagrass occur around Low Isles, Green Island and Cairns Harbour. Intertidal seagrass meadows in the region are situated along nearshore sand and mud banks and mostly consist of Halodule uninervis and Halophila dominated meadows. In Cairns Harbour however, meadows are dominated by Zostera capricorni. Shallow subtidal coastal meadows consist of Halodule uninervis and Halophila communities mostly found along the sheltered coasts and harbours. Cymodocea spp., Thalassia hemprichii, Syringodium isoetifolium and a suite of Halophila species dominate intertidal reef platform habitats of this region.
Seagrass meadows throughout the region are characterised by low nutrient concentrations and are primarily nitrogen limited. Nitrogen inputs to marine waters can therefore directly promote seagrass growth. The indirect consequences of high sediment and nutrient runoff can on the other hand detrimentally influence seagrass distribution and seasonality in the region. From December to March (wet season) low seagrass abundance often coincides with high rainfall and high loads of sediments and nutrients to nearshore marine waters. Sediments and nutrients decrease light availability for seagrass by reducing light penetration in the water column and promoting the growth of algae that can shade seagrass blades. Warm water temperatures during summer also promote growth of algae and can lower productivity of seagrass meadows. Coupled with physical disturbance from storm activity seagrass growth and abundance may therefore be severely depleted over the wet season. Seagrass meadows are generally most abundant in October-November following the dry season that has more favorable light and temperature conditions.
Monitoring of intertidal seagrass meadows occurs in three seagrass habitat types in the region: coastal, reef and estuarine.
Below is a conceptual diagram of coastal seagrass habitat in the Cairns region – major controls are pulsed terrigenous runoff from seasonal rains, salinity and temperature extremes, and sediment disturbance.

Below is a conceptual diagram of reef seagrass habitat in the Cairns region. Shallow unstable sediment, fluctuating temperature, and variable salinity in intertidal regions characterize these habitats. Physical disturbance from waves and swell and associated sediment movement primarily control seagrass growing in these habitats. Reef seagrass habitats in the region are often adjacent to areas of high tourism use and boating activity with propeller and anchor scarring impacts. Globally, nutrient concentrations are generally low in reef habitats due to the coarse nature of the sediments coral sand. In these types of carbonate sediments the primary limiting nutrient for seagrass growth is generally phosphate. This is due to the sequestering of phosphate by calcium carbonate sediments. In this region seagrass meadows inhabiting the near shore inner reefs and fringing reefs of coastal islands inhabit a mixture of terrigenous and carbonate sediments, such as Green Island. Seagrasses at this location have been shown to be nitrogen limited (Udy et al. 1999).

Below is a conceptual diagram of estuarine seagrass habitat in the Cairns region. These habitats are also closely associated with mangrove forests, characterised by fine sediments and prone to high sedimentation and anoxic conditions. The physical and biological connectivity between these habitats is of high importance to support the detrital food chains and the productive faunal communities. The dominant influence of estuary habitats is terrigenous runoff from seasonal rains. Increased river/creek flow results in higher sediment loads which combine with reduced light to create potential light limitation for seagrass (McKenzie 1994). Estuary habitats also have higher loadings of micro and macro-algal epiphytes than those in other seagrass habitats. Salinity fluctuations and scouring make estuary and inlet habitats a seasonally extreme environment for seagrass growth. Estuary habitats also include the ports and shipping activities (including dredging).

Within seagrass canopy water temperatures
Mean within seagrass canopy water temperatures were generally within the 22 – 31°C range, with highest mean temperatures in the late Dry and Monsoon seasons. Extreme within seagrass canopy water temperature (41.5°C) was recorded at YP1 on the 5th February 2008. Over the last 12 months maximum mean temperatures were recorded in February (30.2°C at Yule Point) and October 2007 during the low spring tides. Temperatures at the coastal and reef-platform locations generally follow a similar pattern.
