• 1996
  Critically Endangered
  (Baillie and Groombridge 1996)
• 1996
  Critically Endangered
• 1994
  Extinct
  (Groombridge 1994)
• 1990
  Vulnerable
  (IUCN 1990)
• 1988
  Vulnerable
  (IUCN Conservation Monitoring Centre 1988)

Syngnathus watermeyeri has been recorded in small numbers and its presence/absence in surveys has fluctuated dramatically since these surveys began. Initial surveys in 1963 found 10 River Pipefish in the Bushmans estuary, 11 in the Kariega estuary and two in the Kasouga estuary (Whitfield 1995). Between 1989 and 1992, intensive surveys were conducted in all three estuaries with no specimens recorded. As a result, S. watermeyeri was listed as officially Extinct in the 1994 IUCN Red List but in 1996 a new breeding population was discovered in the East Kleinemonde estuary (Cowley 1998). This new population, however, was declared locally extinct in 2003 when a large flood was thought to have washed their preferred eelgrass habitat out to sea, no specimens have since been found in the East Kleinemonde (James et al. 2008).

The most recent surveys occurred in 2006 and found juvenile S. watermeyeri once again in its historic range (Bushmans, Kariega and Kasouga estuaries) where it had not been reported for over four decades (Whitfield and Bruton 1996). These intensive surveys found a total of 20 juvenile specimens in the Kariega estuary, ranging from 0.05 to 0.2 individuals per square metre (Vorwerk et al. 2007). No mature individuals were found. Peaks in abundance were found in areas where mesohaline conditions prevailed and the percentage vegetation cover exceeded 80% (Vorwerk et al. 2007).

Syngnathus watermeyeri relies on freshwater pulses which provide the nutrients that enable phytoplankton development and, together with particulate organic material brought down by the rivers, support the zooplankton community upon which these pipefish depend for food. The construction of dams and other impoundments have caused a deprivation of fresh water pulses and a subsequent decline in food supply (Whitfield 1995). Dry conditions in the last few years have caused the Kariega river to stop flowing, which will likely result in the absence of S. watermeyeri in this system once again (A.K.Whitfield pers. comm.).

This species may also be particularly susceptible to hypersaline conditions and to large flood events (Vorwerk et al. 2007). A flood event in the East Kleinemonde estuary in 1996 (Cowley 1998) resulted in the apparent localized extinction of S. watermeyeri. This was thought to be the result of primary S. watermeyeri habitat, submerged eelgrass beds, being flushed out to sea (Vorwerk et al. 2007).

The South African National Water Act 1998 (Act 36) requires that all rivers should have an Ecological Reserve amount set aside. The Ecological Reserve relates to "the water required to protect the aquatic ecosystems of the water resource", including both rivers and estuaries (Vorwerk et al. 2008a). Ecological reserves have been determined for some systems in South Africa but not for any estuaries inhabited by S. watermeyeri. When dams were built on the Kariega and its tributary rivers, a water release policy was issued for downstream agriculture but the environmental requirements of estuaries and rivers were not included (Vorwerk et al. 2008a).