Environmental monitoring is an essential feature of environmental assessment and natural resource management. Whilst the focus of monitoring programs is often on the response of chosen variables to a disturbance of particular concern, it is also important to consider the variability of disturbance pressures in relation to the variability of the ecosystem state. In this paper, we discuss the need to relate environmental variability to disturbance variability in small-scale monitoring programs designed to assess the impact of short-term pulses of visitors on the condition of aquatic ecosystems in protected areas. We use data from protected areas from six Koppen climate zones in Australia to highlight the fact that peaks in visitation do not always coincide with existing monitoring protocols or with optimal times for monitoring on the basis of environmental variability, particularly in relation to rainfall and temperature and, hence, likely biological activity. We highlight how recognising the interaction between disturbance variability and environmental variability will greatly enhance the power of monitoring programs and substantially improve our capacity to detect responses to temporally pulsed disturbances. Analyses of this type, undertaken before the establishment of monitoring programs, will yield higher quality information and a better return on monitoring investment for natural resource managers.