The common method to estimate lake levels is the water balance equation, where water input and output result in lake storage and water level changes. However, all water balance components cannot always be quickly assessed, such as due to significant modification of the catchment area. A method that assesses general changes in lake level can be a useful tool in examining why lakes have different lake level variation patterns. Assessment of wetlands using the dynamics of the historical hydrological and hydrogeological data set can provide important insights into variations in wetland levels in different parts of the world. A case study from a saline landscape, Lake Buninjon, Australia, is presented. The aim of the present study was to determine how climate, river regime, and lake hydrological properties independently influence lake water levels and salinity, leaving the discrepancy, for the effect of the non-climatic/catchment modification in the past and the model shows that surface inflow is most sensitive variable. The method, together with the analysis and interpretation, might be of interest to wider community to assess its response to natural/anthropogenic stress and decision choices for its ecological, social, scientific value, and mitigation measures to safe guard the wetland biodiversity in a catchment basin.