Subglacial lake water-volume changes produce ice-elevation anomalies that provide clues about water flow beneath glaciers and ice sheets. Significant challenges remain in the quantitative interpretation of these elevation-change anomalies because the surface expression of subglacial lake activity depends on basal conditions, rate of water-volume change, and ice rheology. To address these challenges, we introduce an inverse method that reconstructs subglacial lake activity from altimetry data while accounting for the effects of viscous ice flow. We use a linearized approximation of a Stokes ice-flow model under the assumption that subglacial lake activity only induces small perturbations relative to a reference ice-flow state. We validate this assumption by accurately reconstructing lake activity from synthetic data that are produced with a fully nonlinear model. We then apply the method to estimate the water-volume changes of several active subglacial lakes in Antarctica by inverting data from NASA’s Ice, Cloud, and land Elevation Satellite 2 (ICESat-2) laser altimetry mission. The results show that there can be substantial discrepancies (20% or more) between the inversion and traditional estimation methods due to the effects of viscous ice flow. The inverse method will help refine estimates of subglacial water transport and further constrain the role of subglacial hydrology in ice-sheet evolution.