Seagrass beds are highly productive and valuable habitats, which fulfill a key role in coastal ecosystems. Spatial distribution, biomass, density, productivity and leaf dynamics of the dominant seagrass species Thalassia testudinum were studied at five locations in the Gandoca-Manzanillo National Wildlife Refuge, Caribbean coast of Costa Rica, from November 2005 until March 2006. Seagrass beds within the study area cover approximately 16 ha. Spatial and temporal differences in ecological seagrass parameters were examined along gradients of riverine inputs and related to a range of environmental parameters (depth, grain size distribution, nutrient concentrations, salinity and temperature). Average canopy cover and above-ground biomass of T. testudinum inversely correlated with depth, but did not vary significantly between study sites when compared along depth ranges. Considerable spatio-temporal variations in shoot densities, areal productivity and leaf sizes seem to be related to riverine inputs and wave energy. It appeared that T. testudinum at exposed sites respond to increased environmental disturbance related to the offset of the rainy season with clonal recruitment, whereby shoot densities increase and average leaf sizes are reduced. Lower shoot densities and greater leaf sizes, in contrast, are characteristic for locations with rather consistent environmental conditions, where seagrasses are sheltered. T. testudinum in the refuge has higher shoot densities but shorter leaves and lower productivity compared to sites in 15 other Caribbean countries. The seagrass beds appear to be in a relatively healthy state, however, observations of temporal increased stocks of filamentous epiphytes and macroalgae indicate temporal environmental stress in the system. Rev. Biol. Trop. 57 (Suppl. 1): 187-201. Epub 2009 November 30.