By 1994, an estimated 1.8 million hectares of cleared land in Western Australia was affected by secondary dryland salinity to some extent. The area affected is likely to double in the coming 20 years. The cause of this salinity is excessive recharge under traditional agriculture, leading to rising groundwater levels. Monitoring changes in groundwater levels is helpful in indicating the degree of threat to agricultural land and public assets. Many researchers have studied groundwater level rises and attempted to explain them statistically.We present an approach for statistically estimating trends in groundwater levels. The approach separates the effect of atypical rainfall events from the underlying time trend and the lag between rainfall and its impact on groundwater is explicitly represented. Rainfall is represented as an accumulation of deviations from average rainfall. Application of the approach is demonstrated using data from 49 bores in Jerramungup Shire, Western Australia. The approach provides high explanatory power, particularly for deeper bores.