River estuary habitats can be subtidal or intertidal, contain many seagrass species, and are often highly productive. In Papua, these habitats are closely associated with mangrove forests, characterized by fine sediments, and prone to high sedimentation and anoxic conditions. The dominant influence of river estuary habitats is terrigenous (from the land) runoff from wet-season rains. Increased river flow results in higher sediment loads that combine with reduced atmospheric light to create potential light limitation for seagrass (McKenzie 1994). Associated salinity fluctuations and scouring make river and inlet habitats a seasonally extreme environment for seagrass growth. Catchments to river estuary habitats often support a large range of land uses, including agricultural, mining, and forestry (logging). These land use practices result in increased sediment inputs (Spalding et al. 2003).

      In river estuary systems, differences in the life history strategies of seagrasses results in varying species assemblages. E. acoroides is a slow turnover, persistent species with low resistance to perturbation (Bridges, Phillips, and Young 1981; Walker, Dennison, and Edgar 1999), suggesting that there are some coastal habitats that are quite stable over time. However, E. acoroides is susceptible to disturbance and it is predicted that removal of a 1 m² area from a meadow would take more than 10 years for full recovery (Rollon et al. 1998). In contrast, C. serrulata, H. uninervis, and H. ovalis are more ephemeral (Birch and Birch 1984). H. uninervis and H. ovalis are considered pioneer species growing rapidly and surviving well in unstable or depositional environments (Bridges, Phillips, and Young 1981; Birch and Birch 1984). C. serrulata grows in deeper sediments, and has been linked to increased sediment accretion (Birch and Birch 1984).

      Coastal habitats are both subtidal and intertidal and support the most diverse seagrass assemblage of all habitat types. Physical disturbance from waves and swell, associated sediment movement, and macro-grazers primarily control seagrass growing in coastal habitats. Episodic events such as cyclones or storms can have severe impacts at local scales, making this a dynamic and variable habitat. Sediment movement due to prevalent wave exposure creates an unstable environment where it is difficult for seagrass seedlings to establish or persist. Areas of seagrass that have been physically removed by a cyclone can take many years to regrow (Preen, Lee Long, and Coles 1995). Succession or recolonization after extreme loss has been suggested to be directional and modified by small-scale perturbations, resulting in patchiness in seagrass distributions (Birch and Birch 1984). Cymodocea and Syringodium are seen as intermediate genera that can survive a moderate level of disturbance, while Halophila and Halodule are described as ephemeral species with rapid turnover and high seed set, well adapted to high disturbance and high rates of grazing (Walker, Dennison, and Edgar 1999). The end result of this successional process, however, varies with geographic location.

      Reef habitats support seagrass communities of high biodiversity and can be highly productive. Fringing reef platforms are almost always intertidal. Shallow unstable sediment, fluctuating temperature, and variable salinity in intertidal regions characterize these habitats. Nutrient concentrations are generally low in reef habitats, however intermittent sources of nutrients are added by seasonal runoff and seabirds. The primary limiting nutrient for seagrass growth (either phosphate or nitrogen) in carbonate sediments can vary between geographic locations around the world (Short, Dennison, and Capone 1990; Fourqurean, Zieman and Powell 1992; Erftemeijer and Middelburg 1993; Udy et al. 1999). Tight nutrient recycling strategies of T. hemprichii (e.g., the location of nitrogen in the rhizomes), aids in survival in the nutrient-poor reef habitat when leaves are shed due to desiccation stress (Stapel, Manuntun, and Hemminga 1997). Reef seagrass communities also have unique faunal interactions. Bioturbation by shrimps can be so prevalent in some reef environments as to prevent seagrass growth (Ogden and Ogden 1982; Tomascik et al. 1997). A region of bare sand often separates coral heads from seagrass meadows; previous research suggests this is maintained by parrotfish and surgeonfish associated with the coral (Randall 1965).

      Deep water seagrasses occur at subtidal depths greater than 10 m, and are restricted to where high water clarity allows sufficient light penetration for photo-synthesis (Lee Long, Mellors, and Coles 1993). Deep water seagrass areas can be extensive and dominated by Halophila species (Lee Long, Mellors, and Coles 1993; Lee Long, Coles, and McKenzie 1996). Large monospecific meadows of seagrass occur in this habitat (e.g., Halophila decipiens), which contrasts with coastal and reef habitats where the seagrass meadows are generally diverse and mixed (Coles et al. 1987). Halophila species display morphological, physiological, and life history adaptations to survive low light conditions. Halophila species have rapid growth rates and are considered opportunistic species (Birch and Birch 1984). H. decipiens has an open canopy structure with relatively little below ground biomass and high leaf turnover and rhizome elongation rates (Josselyn et al. 1986; Kenworthy et al. 1989). Halophila species also have high seed production. For example, Kuo and Kirkman (1995) reported H. decipiens seed banks of 176,880 seeds per m². The distribution of deep water seagrasses, while mainly influenced by water clarity, is also modified by seed dispersal, nutrient supply, and current stress. Although the ecological role of deep water seagrasses is poorly understood, some deep water meadows are important dugong feeding habitat (Lee Long, Coles, and McKenzie 1996; Marsh and Saalfeld 1989; Anderson 1994). Unfortunately, deep water systems are the least understood seagrass community.

      The four broad groups of seagrass habitats in Papua contain a large range of life history strategies, which provides some insight into the dynamic but variable physical nature of Papuan seagrass habitats. The species present in the different habitats reflect the observed physical and biological impacts, suggesting that reef, deep water, and coastal environments are particularly variable and dynamic, while estuarine habitats have stable areas but are extremely harsh. Of these seagrass habitat types in Papua, both estuarine (including large shallow lagoons) and coastal seagrass habitats are of primary concern with respect to water quality due to their location immediately adjacent to catchment inputs.

      Papuan Seagrasses

      Papua includes the most eastern province of Indonesia (formerly known as Irian Jaya) and extends west from the northeast border of Papua New Guinea to Halmahera