The glacial aquifer system in the United States is a major source of water supply but previous work on historical groundwater trends across the system is lacking. Trends in annual minimum, mean, and maximum groundwater levels for 205 monitoring wells were analyzed across three regions of the system (East, Central, West Central) for four time periods: 1964–2013, 1974–2013, 1984–2013, and 1994–2013. Trends were computed separately for wells in the glacial aquifer system with low potential for human influence on groundwater levels and ones with high potential influence from activities such as groundwater pumping. Generally there were more wells with significantly increasing groundwater levels (levels closer to ground surface) than wells with significantly decreasing levels. The highest numbers of significant increases for all four time periods were with annual minimum and/or mean levels. There were many more wells with significant increases from 1964 to 2013 than from more recent periods, consistent with low precipitation in the 1960s. Overall there were low numbers of wells with significantly decreasing trends regardless of time period considered; the highest number of these were generally for annual minimum groundwater levels at wells with likely human influence. There were substantial differences in the number of wells with significant groundwater-level trends over time, depending on whether the historical time series are assumed to be independent, have short-term persistence, or have long-term persistence. Mean annual groundwater levels have significant lag-one-year autocorrelation at 26.0% of wells in the East region, 65.4% of wells in the Central region, and 100% of wells in the West Central region. Annual precipitation across the glacial aquifer system, on the other hand, has significant autocorrelation at only 5.5% of stations, about the percentage expected due to chance.