Abstract1. Recent data on habitat characteristics and the animal and plant communities from 166 brackish lagoons in Great Britain have been analysed to interpret their community stucture and the environmental features important to maintaining the diversity of specialist lagoonal species.2. Lagoons supporting a diverse community of specialist species of restricted distribution are considered to be the most valuable in conservation terms.3. Lagoons are concentrated in the south and east of the country, are predominantly shallow with fine sand and mud sediments and cover a range of sea‐inlet types, areas and salinities (from zero to hyperhaline).4. The environmental characteristics of lagoons show more variability than those of ambient sea‐or estuarine water.5. Six suites of species are identified: freshwater species, stenohaline marine lagoonal specialists, euryhaline lagoonal specialists, estuarine species tolerant of lagoons, estuarine species incidental in lagoons and underrecorded species.6. The lagoons are categorized as freshwater sites and groups of saline sites of a range of conservation value in terms of their community, from high value sites dominated by stenohaline specialist species to sites supporting no specialist lagoonal community.7. The higher value sites are bar‐built or sluiced lagoons with a channel inlet, with salinities close to 35%0, a heterogeneous sediment, predominantly shallow and with larger area if narrow. Spatial density of lagoons may be important in recruitment of stenohaline specialist species, and frequent exchange of a proportion of the lagoon water with adjacent estuary or sea‐water may be important in maintaining requisite salinity.8. Aspects worthy of further study are ide