Estimation of effective population sizes (Ne) and temporal gene flow (Nem, m) has many implications for understanding population structure in evolutionary and conservation biology. However, comparative studies that gauge the relative performance of Ne, Nem or m methods are few. Using temporal genetic data from two salmonid fish population systems with disparate population structure, we (i) evaluated the congruence in estimates and precision of long- and short-term Ne, Nem and m from six methods; (ii) explored the effects of metapopulation structure on Ne estimation in one system with spatiotemporally linked subpopulations, using three approaches; and (iii) determined to what degree interpopulation gene flow was asymmetric over time. We found that long-term Ne estimates exceeded short-term Ne within populations by 2–10 times; the two were correlated in the system with temporally stable structure (Atlantic salmon, Salmo salar) but not in the highly dynamic system (brown trout, Salmo trutta). Four temporal methods yielded short-term Ne estimates within populations that were strongly correlated, and these were higher but more variable within salmon populations than within trout populations. In trout populations, however, these short-term Ne estimates were always lower when assuming gene flow than when assuming no gene flow. Linkage disequilibrium data generally yielded short-term Ne estimates of the same magnitude as temporal methods in both systems, but the two were uncorrelated. Correlations between long- and short-term geneflow estimates were inconsistent between methods, and their relative size varied up to eightfold within systems. While asymmetries in gene flow were common in both systems (58–63% of population-pair comparisons), they were only temporally stable in direction within certain salmon population pairs, suggesting that gene flow between particular populations is often intermittent and/or variable. Exploratory metapopulation Ne analyses in trout demonstrated both the importance of spatial scale in estimating Ne and the role of gene flow in maintaining genetic variability within subpopulations. Collectively, our results illustrate the utility of comparatively applying Ne, Nem and m to (i) tease apart processes implicated in population structure, (ii) assess the degree of continuity in patterns of connectivity between population pairs and (iii) gauge the relative performance of different approaches, such as the influence of population subdivision and gene flow on Ne estimation. They further reiterate the importance of temporal sampling replication in population genetics, the value of interpreting Neor m in light of species biology, and the need to address long-standing assumptions of current Ne, Nem or m models more explicitly in future research.