Measurement of allele frequency shifts between temporally spaced samples has long been used for assessment of effective population size (N-e), and this 'temporal method' provides estimates of N-e referred to as variance effective size (N-eV). We show that N-eV of a local population that belongs to a sub-structured population (a metapopulation) is determined not only by genetic drift and migration rate (m), but also by the census size (N-c). The realized N-eV of a local population can either increase or decrease with increasing m, depending on the relationship between N-e and N-c in isolation. This is shown by explicit mathematical expressions for the factors affecting N-eV derived for an island model of migration. We verify analytical results using high-resolution computer simulations, and show that the phenomenon is not restricted to the island model migration pattern. The effect of N-c on the realized N-eV of a local subpopulation is most pronounced at high migration rates. We show that N-c only affects local N-eV, whereas N-eV for the metapopulation as a whole, inbreeding (N-eI), and linkage disequilibrium (N-eLD) effective size are all independent of N-c. Our results provide a possible explanation to the large variation of N-e/N-c ratios reported in the literature, where N-e is frequently estimated by N-eV. They are also important for the interpretation of empirical N-e estimates in genetic management where local N-eV is often used as a substitute for inbreeding effective size, and we suggest an increased focus on metapopulation N-eV as a proxy for N-eI.