The reproduction of Saltwater Crocodiles (Crocodylus porosus) is seasonal, coinciding with the wet season (October–May) in the Northern Territory, Australia. Understanding environmental factors influencing the population dynamics of C. porosus can have important implications for the management of this species. We examined the relationship between hatchling density and monthly rainfall in the preceding wet season using crocodile population data from standardized spotlight surveys in 10 tidal rivers from 1976 to 2012 and historical weather data. Hatchling densities in four rivers were negatively correlated with monthly rainfall around the peak of the wet season (January or February). Hatchling densities in four rivers were positively correlated with rainfall after the peak months. Hatchling densities in eight rivers were positively correlated with rainfall after the wet season peak (April or May). Our results support previous observations that: (1) the length of the wet season determines the extent of reproduction; and (2) flooding caused by heavy rains in the middle of the wet season leads to higher rates of egg mortality. These relationships could be used to estimate reproductive success from year to year, and to guide management decisions such as adjusting the harvest intensity of eggs and hatchlings.