Benthic algal biomass depends on a number of variables, including local factors such as the ionic water composition, nutrient availability, light, or water velocity, and large-scale factors such as the drainage area and land uses in the watershed. The relative roles of local and large-scale factors affecting benthic chlorophyll variation were analyzed in the Guadiana watershed by means of variation partitioning and partial least squares regression. The potential relevance of 20 physical, chemical and physiographical variables was analyzed throughout the watershed, and separately in three distinct geological units: upper watershed calcareous streams, streams with siliceous bedrocks, and the main river reaches. Our results suggest that many predictors of algal biomass are intercorrelated but have independent effects, and that their importance varies between geological units. Nutrient content and land uses exerted the largest influence on the pattern of chlorophyll-a variation in the three ecotypes studied ; Additional funding was obtained from the projectsSCARCE (Consolider Ingenio 2010, CSD2009-00065) and CARBONET(CGL2011-30474-C02-01) of the Spanish Ministry of Science andInnovation