The distribution of Solea solea and Solea senegalensis in the Tagus estuary was studied following a small-scale approach. Preliminary sampling revealed that sole concentrated in two areas within their nursery grounds, the main subtidal channel and a large intertidal mudflat. Beam trawls were conducted intensively in the two areas in July 2006. Depth, salinity and water temperature were measured. Substrate samples were collected for sediment type determination and macrobenthos identification and quantification. Generalized linear models were applied in order to explain the occurrence and variability of soles' densities, using depth, salinity, water temperature and abundance of polychaetes, oligochaetes, amphipods, isopods and bivalves as explanatory variables. While S. solea was more abundant in the main subtidal channel, a deeper, warmer and lower salinity area, S. senegalensis abundance was highest at the intertidal mudflat area. Presence of both species in the two areas was associated with abundance of polychaetes (generally with another variable associated), and for S. senegalensis in the subtidal channel it was associated with amphipods and depth. Abundance of S. solea in the main subtidal channel was associated mainly with polychaetes abundance, while that of S. senegalensis was associated with amphipods density. In the intertidal mudflat, bivalves and polychaetes presented significant relationships with both species densities. Some of the factors that had been reported to be important for the distribution of these species in previous studies also do so at a finer scale; however, this small-scale approach provided an in-depth knowledge on habitat selection and spatial segregation of these species within this nursery area.