Four compartments of a salmonid brook were studied in consecutive sections either at sector scale or at facies scale: physical features, water quality, macrophytes and salmonids. The most important factor in the spatial and temporal organisation was the longitudinal zonation assessed by the four compartments. It was mainly shown by a gradient of the length of the morphodynamic sequence and of the facies width, of the pH and the conductivity and of macrophyte cover. It induced a colonisation by older trout in the downstream part of the brook where growth was better and shelter given by the bankside vegetation was more abundant. There were also greater densities of other age-classes upstream, with a correlation between salmon and rock shelter. Furthermore, the second factor corresponded to the flow characteristics and a granulometry gradient. The third factor corresponded chiefly to lighting, salmon numbers and densities. Salmonids showed a temporal stability from spring to autumn, and an opposition between growth and density. Six clusters of sectors defined functional entities. With regard to the 3-dimensional structure of the brook, the special pattern of each compartment shows its contribution to the functioning of the whole. Taking into account the scale of the study, the coexistence between trout and salmon did not show a competition between the two species, but rather a spatial partition, thanks to the heterogenity inside each sector. We concluded on the necessity of studying sympatry at the facies scale to assess the role of habitat factors as regulators of carrying capacity.