Major breeding grounds include Tung Chung Bay and the waters around Tap Mun (Grass Island), including Hoi Ha Wan Marine Park and Fung Wong Wat, according to the Eco-Education & Resources Centre and Green Power study.
The findings shed light on the local distribution of the horse-like fish, once thought to breed only in saltwater coral reefs.
Centre founder Ken Ching-see ho said the study offers evidence that river estuaries are of high ecological importance for conserving biodiversity.
"We hope the government will take this into account when carrying out development near rivers as land reclamation will have a destructive effect on the marine habitats of these species," Ching said.
The groups examined 33 locations across the city and found seahorses and pipefish favoured shallows about seven metres in depth with a seabed of coarse sand, mud, rock or coral reef.
But many of the most thriving habitats were also located near freshwater inflows, Ching said. "We are not ruling out the possibility that food at river mouths could be more abundant."
Key habitats for rare spotted seahorses include several areas in Port Shelter south of Sai Kung, such as Shelter Island, Kiu Tsui Chau (Sharp Island), Kau Sai Chau and Pan Long Wan.
Seahorses were also found in coastal areas around Tolo Harbour and Channel in the northeast New Territories, including Lung Mei and Yeung Chau in Plover Cove, Kei Ling Ha Hoi (Three Fathoms Cove), Hoi Ha Wan, Lo Fu Wat, Fung Wong Wat and Tap Mun.
For the first time, the group also reported sightings of seaweed pipefish near Mirs Bay, including at Kat O (Crooked Island) and Ping Chau.
To the west, between Lantau Island and Chep Lap Kok Airport, seaweed pipefish were spotted in Tung Chung Bay, Hau Hok Wan and Sha Lo Wan.
Ching said many of the key habitats were under threat from rapid development. Worldwide, seahorses and pipefish risk being overfished for use in traditional medicine or for aquariums.
Since 2012, green groups have criticised a government plan to turn Lung Mei, located near the Plover Cove Reservoir, into a man-made beach. The Save Lung Mei Alliance said it was home to about 200 species of marine animals, including the rare spotted seahorse.
The trading of all seahorse species is regulated under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES).
But the Agriculture, Fisheries and Conservation Department does not keep a record of seahorse distribution or numbers, nor does it lead any conservation programmes.
A spokeswoman for the department said two species of seahorse have been recorded in Hong Kong: the spotted seahorse and the three-spot seahorse.