Biophysical models are used to predict the spatial distributions of organisms. Nevertheless, understanding factors influencing the temporal distributions of animals may often be additionally required. It is expected that intertidal macrofauna of the wet–dry tropics face a multitude of temporal challenges because there is not only seasonal drying but also variation in surface moisture over the circatidal cycle. Activities of fiddler crabs (Uca spp.) depend on adequate surface moisture being available for feeding and respiration. A recent study monitored crab abundance during spring tides and found that one Uca species in the mangroves of Darwin Harbour, Australia, U. flammula, is most abundant in the wet season, while another, U. elegans, is most abundant in the dry season. We hypothesized here that these seemingly contradictory abundance patterns are driven by temporal variation in the availability of soil moisture within each species habitat. We thus monitored crab abundance and measured soil moisture content across four types of habitat (low gap centres, low gap edges, mid-height gap centres and high gap centres) seasonally and across the circatidal cycle. We found that crab abundance and soil moisture both varied over time among habitat types. We used a log-linear model to show that habitat type influenced soil moisture and this in turn influenced crab abundance. Sampling across the circatidal cycle showed that U. flammula was more abundant in the wet season, as reported previously, while the abundance of U. elegans did not vary between seasons. Our model suggested that U. elegans ‘makes up for lost time’ in the dry season by undertaking all activities during spring tide low water as only at this time is the substratum moist enough for feeding and respiration. We highlight the importance of measuring multiple variables across habitats over small and large scales when assessing temporal abundance patterns of intertidal tropical organisms.