1. Seahorses are marine fish with several life history characteristics hypothesized to make them resilient but are of conservation concern because of their international trade and habitat loss.
2. Surveys of two unexploited European seahorse species (Hippocampus guttulatus and Hippocampus hippocampus) in Ria Formosa lagoon, Portugal, were repeated seven years after their populations in the lagoon were found to be among the densest in the world.
3. Population densities of both species declined significantly between 2001/2002 and 2008/2009 surveys (94% and 73% for H. guttulatus and H. hippocampus respectively). H. guttulatus declines were not associated with any environmental changes measured (i.e. percentage live benthic habitat cover, depth, temperature, water current speed, horizontal visibility). H. hippocampus declined more where current speed had decreased.
4. At the low densities found in 2008/2009, occurrence for both species was best predicted by depth: seahorses were found in deeper locations throughout the lagoon. Other important predictors were temperature for H. guttulatus (found at sites warmer than average) and current speed for H. hippocampus (found in locations with faster currents).
5. The large declines in seahorse densities made it difficult to compare results over time. Presence–absence and abundance modelling at multiple scales can help to ensure that data are comparable even when populations fluctuate drastically.