Groundwater levels represent the aggregation of different hydrological processes acting at multiple spatial and temporal scales within aquifer systems. Analyzing trends in groundwater levels is therefore essential to quantify available groundwater resources for beneficial use, and to devise plans/policies to better manage these resources. In this work, three trend analysis methods are employed to detect long-term (1971–2021) trends in annual mean/minimum/maximum depth to water table (DTW) at 910 bores. This analysis is performed in eight main alluvial systems in the Murray–Darling Basin (MDB), Australia, which concentrate nearly 75% of groundwater use. The results show: (a) an overall increasing trend in DTW across alluvial aquifers attributable to changes in recharge from rainfall and groundwater extraction; (b) the analysis methods employed show similar statistical significances and magnitudes, but differences exist; (c) the annual minimum DTW has a smaller trend magnitude than annual mean DTW, and the annual maximum DTW has a larger trend magnitude than mean DTW; (d) trends in annual rainfall and potential evaporation, and cumulative number of production bores, are consistent with the groundwater trends; (e) irrigation is responsible for some of the decreasing trend in groundwater level. These results could be used to target further research and monitoring programs, and inform groundwater resource management decisions in the MDB.