Abstract Salmonids are introduced in various ecosystems, including mountain lakes characterised by extreme environmental constraints. Although these constraints can affect salmonid body condition through direct and indirect pathways, they remain seldom explored despite their importance for understanding salmonid fitness and long‐term establishment. In order to fill this gap, we firstly fitted species‐specific weight–length relationships for three salmonid species in nine mountain lakes, and compared their allometric coefficients with those of 362 salmonid populations worldwide to identify potential differences in growth trajectory of salmonids in the studied lakes. We then investigated how thermal characteristics and lake morphometry could influence salmonid body conditions, both directly and indirectly through salmonid density, the presence of forage fish and resource densities. We calculated salmonid relative body condition Kn and used a structural equation model (SEM) to disentangle these direct and indirect effects. The values of allometric coefficients for the three species did not differ from those of most salmonids worldwide although ontogenetic changes in Salvelinus alpinus weight gain was observed. Kn differed significantly among the populations studied. The strongest effects were related to direct and indirect effects of lake morphometry, while thermal characteristics had mostly indirect effects on Kn . The strength and the sign of the indirect effects of morphometry and temperature were mediated by the direct effects of resource and salmonid densities on Kn . Kn estimates were greater in lakes with shallow basin slopes than those with steep slopes. Shallow basin slopes probably provide habitats that support high prey availability and require lower energy expenditure by salmonids compared to lakes with steep slopes dominated by pelagic habitats. Complementarily, higher winter and summer temperatures favour Kn by supporting higher prey densities and longer periods of feeding activity. Our results may help managers to select lakes that optimise sustainability of salmonid populations based on the joint effects of basin morphometry and the expected thermal modifications induced by global change.