I examined the relationship between landscape attributes and population differentiation among lake trout (Salvelinus namaycush) populations inhabiting a hierarchically structured dendritic freshwater system in northern Labrador, the Kogaluk River system. Samples were collected from a total of 10 lakes which differed in size, elevation, level of connectivity, and position within the system. STRUCTURE analysis provided evidence of significant population structure within the system likely attributed to a varying degree of asymmetric gene flow. Gene flow estimates were generally low and appear to be influenced by the presence of waterfalls as well as geographic distance. Isolation by distance tests coupled with decomposed pairwise regression analysis suggest a significant influence of geographic distance on population differentiation. Mantel testing also showed that population differentiation is significantly correlated with the position of waterfalls. Estimates of effective population size reveal significantly smaller population sizes in headwater lakes, a pattern not attributed to lake size.