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Understanding the temporal and spatial roles of nutrient limitation on phytoplankton growth is necessary for developing successful management strategies. Chesapeake Bay has well-documented seasonal and spatial variations in nutrient limitation, but it remains unknown whether these patterns of nutrient limitation have changed in response to nutrient management efforts. We analyzed historical data from nutrient bioassay experiments (1992–2002) and data from long-term, fixed-site water-quality monitoring program (1990–2017) to develop empirical approaches for predicting nutrient limitation in the surface waters of the mainstem Bay. Results from classification and regression trees (CART) matched the seasonal and spatial patterns of bioassay-based nutrient limitation in the 1992–2002 period much better than two simpler, non-statistical approaches. An ensemble approach of three selected CART models satisfactorily reproduced the bioassay-based results (classification rate = 99%). This empirical approach can be used to characterize nutrient limitation from long-term water-quality monitoring data on much broader geographic and temporal scales than would be feasible using bioassays, providing a new tool for informing water-quality management. Results from our application of the approach to 21 tidal monitoring stations for the period of 2007–2017 showed modest changes in nutrient limitation patterns, with expanded areas of nitrogen-limitation and contracted areas of nutrient saturation (i.e., not limited by nitrogen or phosphorus). These changes imply that long-term reductions in nitrogen load have led to expanded areas with nutrient-limited phytoplankton growth in the Bay, reflecting long-term water-quality improvements in the context of nutrient enrichment. However, nutrient limitation patterns remain unchanged in the majority of the mainstem, suggesting that nutrient loads should be further reduced to achieve a less nutrient-saturated ecosystem.