There are four estuaries within the Nelson City area.
- The internationally recognised Waimea Inlet which straddles the Nelson City and Tasman District Council boundary
- The Nelson Haven, fed by the Maitai River and home to Port Nelson
- Delaware Estuary, framed by Pepin Island and Delaware Spit
- Kokorua Estuary to the north - only accessible by boat or with permission of landowners.
Estuaries are remarkable ecosystems teeming with life and critical to the lifecycle of many aquatic species. They are also home to a number of native and migrant birds.
The Waimea Inlet is of international importance for species such as the variable oystercatcher and migratory species such as wrybill and bar-tailed godwit. It is also significant within New Zealand for its banded rail and Caspian tern populations. The Waimea Inlet also has a number of small sand islands, e.g. Saxton, Oyster, Pig and Sand Island, which are important habitat for shorebirds to roost and feed.
Shorebird surveys at the Top of the South Island have been undertaken by members of the Ornithological Society of New Zealand (OSNZ) since 1961. The OSNZ report Shorebirds of Farewell Spit, Golden Bay and Tasman Bay (2013) summarises the distribution and numbers of shorebirds between 2001 and 2012, and areas of international importance for the Nelson-Tasman region.