A densely vegetated area along the land edge (terrestrial margin) of estuaries serves multiple important functions. It filters and absorbs sediment and nutrients, acts as a barrier against invasive grasses and weeds, and provides food and habitat for various species. In riparian zones, which are areas adjacent to waterways, this vegetation also offers shade that helps to regulate stream temperatures.

The 200m terrestrial margin of Catlins Estuary is primarily high-producing (38%) and low-producing grassland (34%). Like the wider catchment, most of the pasture supports sheep and beef grazing, with a small area of dairying west of Pounawea. In some areas (e.g., Catlins Lake), pasture within the margin was historically wetland or salt marsh habitat. Only ~20% of the margin was densely vegetated, including two areas of remnant indigenous forest in the lower estuary.

There have been no significant changes in the 200m terrestrial margin between 2016 and 2023. Small differences between surveys are attributed to the reclassification of some features (e.g., grassland and herbaceous saline vegetation) following more extensive ground-truthing and access to higher resolution aerial photographs in 2023.

Mud is a significant stressor on estuary habitats as it can smother seagrass and shellfish beds and displace sensitive species. Muddy sediments can also concentrate contaminants, nutrients, and organic matter, leading to the deterioration of sediment condition (i.e., low sediment oxygen levels) and a reduction in habitat quality for estuary macrofauna.

Sandy sediments dominate throughout the lower estuary and in the east of Catlins Lake. Mud-elevated sediments (>25% mud content, condition rating of ‘Poor’), which are generally associated with degraded ecological health, comprised ~25% of the available intertidal habitat (area outside of salt marsh). These areas were primarily located near the mouths of Catlins River, the Ōwaka River, and other small freshwater inputs, and within small embayments. Many of these areas contained very soft sandy muds (50-90% mud), often associated with poor sediment oxygen levels and nuisance macroalgal growth. There was no significant change in dominant substrate types between 2016 and 2023, although 2023 results indicated a decrease in the muddiness of sand habitat throughout the central reaches of the estuary.

Salt marsh is important in estuaries as it is a highly productive habitat. It naturally filters and assimilates sediment and nutrients, mitigates shoreline erosion, and provides an important habitat for a variety of species including insects, fish and birds.

The estimated historical extent of salt marsh is ~64ha or 11% of the intertidal area. Since the 1900’s, substantial losses have occurred, particularly near the Catlins River mouth, due to drainage, roading infrastructure and conversion to pasture. More recently, losses have occurred in the lower estuary on a large sand-spit near Cabbage Point (across the channel from Pounawea). In this area, small pockets of historic salt marsh have gradually eroded away, until fully disappearing by the early 1990’s. Salt marsh extent has not significantly changed between 2006 and 2023. Current salt marsh extent represents only 21% of the estimated natural extent (a condition rating of ‘Poor’)

Seagrass (Zostera muelleri) habitat is important in estuaries because it provides a nursery and feeding ground for many organisms, including sediment fauna and fish. Seagrass also enhances primary production and nutrient cycling, and stabilises sediments. Seagrass habitats are vulnerable to muddy sediment and excess nutrient inputs from the catchment, with impacts including reduced light availability and smothering by macroalgae blooms, and physical impacts such as scouring, vehicle damage, and swan grazing.

Historically seagrass was scarce in the lower estuary near the entrance, and more extensive in Catlins Lake, with beds expanding in this area between 1948 and 1985. Since 1995, no high (≥50%) cover seagrass has been evident in Catlins Lake (based on available imagery). A large sand spit that extended from the southern side of the estuary at Cabbage Point towards the Ōwaka River mouth historically reduced tidal flushing in the lower estuary. Coincident with its erosion was an expansion of seagrass upstream and downstream of this area. Since 2006 there has been little change in the overall footprint in which seagrass is growing, although there has been a 47% loss in high (≥50%) cover seagrass attributed to erosion and fragmentation of beds near Pounawea (primarily from river scouring and flood impacts), and natural variability of beds near the river channel and in the mobile sands near the estuary entrance.

Macroalgae (aka seaweed) is a natural feature of estuaries, however excess nutrient inputs can lead to persistent and widespread macroalgal blooms. At nuisance levels, macroalgae can form mats that can adversely impact the underlying sediments, smother seagrass and displace sensitive species.

Since 2016, macroalgal blooms have caused increasingly widespread adverse impacts on the estuary. Aerial imagery indicates persistent blooms first appeared in 2010 in two small embayments northwest of the Hinahina Road bridge, before expanding more widely into the upper Catlins Lake, the Ōwaka Arm and within small embayments on the southern margin of the lower estuary. By 2021, both macroalgal extent and biomass in these areas had significantly increased and in 2023, some areas had become so degraded that macroalgae were no longer able to survive. Extensive blooms of a brown filamentous alga, similar to Pylaiella littoralis, was recorded for the first time in 2023.