In order to examine the effect of habitat size variability on density-dependent population dynamics, we developed a general population model in which changes in population abundance, density, and habitat size are taken into account. From this model, we deduced several predictions for patterns and processes of population dynamics. We tested these predictions by applying our model to population dynamics data of 36 populations of Tigriopus japonicus, a marine copepod inhabiting tide pools of variable sizes caused by weather processes. As expected, we found a significant difference in the fluctuation patterns of population abundance and density of T. japonicus populations with respect to the correlation between abundance and density and their relative variability, which correlates positively with the variability of habitat size. In addition, we found direct and lagged-indirect effects of weather processes on population growth, which were associated with density dependence and impose regulatory forces on local and regional population dynamics. We suggest that without knowledge of habitat size fluctuation, measures of population size and its variability as well as inferences about the processes of population dynamics may be misleading.