Generally, there is little known about the in situ ecology of H. abdominalis. In Australia, there is on-going research on populations in the Derwent Estuary, Tasmania and Sydney Harbour, NSW (K. Martin-Smith, pers. comm.). Most NZ research has focused on aspects of diet and reproduction, conducted ex situ on wild individuals from Wellington Harbour (Woods 2002 and 2005, Poortenaar et al. 2004).

Habitat:
Adult Hippocampus abdominalis have been recorded from harbours, protected coastal bays and deep waters with sponges (Kuiter 1993, Kuiter 2001). Depth range varies considerably from the surface down to 104 m (Amaoka et al. 1990, Paulin and Roberts 1992, Francis 1998, Lourie et al. 1999, Stevenson and Beentjes 2001). Habitat varies from intertidal rock pools to, more commonly, amongst shallow macroalgal stands (e.g., Ecklonia, [Kuiter 2000]), submerged rocky outcrops, exposed open sea floor and artificial structures (Francis 1998, Woods 2003). In Tasmania, H. abdominalis are reported as common near the entrances of large estuaries on muddy bottoms, or near reef edges, feeding on small crustaceans (Last et al. 1983). It is not definitively known whether they occupy home ranges or are free-ranging, although some evidence suggests certain populations may exhibit site fidelity (Van Dijken 2001). Unlike most seahorse species, H. abdominalis is a relatively strong swimmer and has been known to swim over hundreds of meters in the course of a day (Vincent 1990). Adults are also known to occur in open water and to raft on macroalgal rafts (Kingsford and Choat 1985) and seagrass (J. Manna, pers. comm.): this occurs at all times of the year in at least New Zealand (Kingsford and Choat 1985, Kingsford 1986). Artificial structures appear to be important habitats for H. abdominalis: in particular, jetties, nets and salmon cages. For example, hundreds of individuals have been observed on anti-predator nets surrounding salmon aquaculture pens in the Huon Estuary, Tasmania (Marshall 2004, K. Martin-Smith, pers. comm.). Similarly, H. abdominalis have been observed in reasonably large numbers on the net of a swimming enclosure in Sydney Harbour since 2003 (K. Martin-Smith, pers. comm.).

Reproduction:
As with other members of the seahorse and pipefish family, males incubate eggs in an abdominal pouch and eventually release young that look like miniature replicas of adults (Edgar 1997). The pouch is developed at about six months of age, but first breeding occurs closer to 12 months (R. Kuiter, pers comm. in Pogonoski et al. 2002). Spawning occurs mainly from (the Austral) spring to summer, where Woods (in press) found brooding males present throughout the year, but with an apparently lower incidence of brooding in winter. Similarly, Poortenaar et al. (2004) examined the reproductive biology of female H. abdominalis, looking at ovarian morphology, reproductive condition and sex steroid levels. Using these indices, they found that females were capable of reproductive activity throughout the year, presenting the potential for a protracted spawning season (Poortenaar et al. 2004).

The number of juveniles (mean ± 1 SE) released per brood in a New Zealand population was 271.2 ± 27 (Woods, in press), whereas the maximum reported brood size for the species in aquaculture is 1,116 (R. Hawkins pers comm. in Lourie et al., 2004). Juveniles 16–19 mm in standard length, are released from the pouch after about thirty days. Larger males produce more juveniles (Woods, in press). Juvenile length and weight are not correlated with the number of juveniles per brood, parent male size or parent male pouch volume. The percentage of pouch contents that are non-viable (i.e., premature or non-viable eggs) upon juvenile release tends to be low (1.1 ± 0.2%; mean ± 1 SE of the total pouch contents) (Woods, in press). Following release from the parent male, juveniles are believed to be pelagic, at least for several weeks, Juveniles up to 8 cm in length have been collected in surface waters of the open ocean over the Chatham Rise in New Zealand (Woods, pers. obs.) and adult H. abdominalis have been captured near-shore associated with floating seaweed and debris (Kingsford and Choat 1985). The propensity for rafting presents a possible large-scale dispersal mechanism for this species.

Diet:
The diet of wild adult H. abdominalis consists largely of crustaceans, in particular amphipods, caridean shrimp, and peracarids (Woods 2002). There are no differences in diet between male and female seahorses. Smaller seahorses consume relatively more crustaceans than larger seahorses, where a greater proportion of their gut contents are comprised of amphipods when compared with adults. There is evidence for seasonal differences in diet, with amphipod consumption peaking in spring and summer, and decapod consumption lowest in autumn (Woods 2002).

Behaviour:
This species is reported to be more active at dusk and at night than during the day in New Zealand (Paulin and Roberts 1992). In Australia, H. abdominalis has been observed aggregating in groups at night (K. Martin-Smith, pers. comm.).