The relationship between the effective number of breeders ( N b ) and the generational effective size ( N e ) has rarely been examined empirically in species with overlapping generations and iteroparity. Based on a suite of 11 microsatellite markers, we examine the relationship between N b , N e and census population size ( N c ) in 14 brook trout ( Salvelinus fontinalis ) populations inhabiting 12 small streams in Nova Scotia and sampled at least twice between 2009 and 2015. Unbiased estimates of N b obtained with individuals of a single cohort, adjusted on the basis of age at first maturation ( α ) and adult lifespan (AL), were from 1.66 to 0.24 times the average estimates of N e obtained with random samples of individuals of mixed ages (i.e. ). In turn, these differences led to adjusted N e estimates that were from nearly five to 0.7 times the estimates derived from mixed-aged individuals. These differences translate into the same range of variation in the ratio of effective to census population size within populations. Adopting as the more precise and unbiased estimates, we found that these brook trout populations differ markedly in their effective to census population sizes (range approx. 0.3 to approx. 0.01). Using A ge N e , we then showed that the variance in reproductive success or reproductive skew varied among populations by a factor of 40, from V k / k ≈ 5 to 200. These results suggest wide differences in population dynamics, probably resulting from differences in productivity affecting the intensity of competition for access to mates or redds, and thus reproductive skew. Understanding the relationship between N e , N b and N c , and how these relate to population dynamics and fluctuations in population size, are important for the design of robust conservation strategies in small populations with overlapping generations and iteroparity.