The quantification of vertical groundwater fluxes across semi-confining layers is fundamental to evaluate groundwater recharge and discharge rates to and from aquifer systems. Methods to estimate vertical groundwater fluxes from temperature–depth profiles have been available since the 1960s. While some methodologies assume steady-state conditions, changes in land-surface temperatures as well as hydrogeological conditions can lead to transient heat flow conditions. Indeed, many studies have indicated that transient temperatures in deeper confined aquifers are widespread. A study is presented that uses transient-temperature–depth curves obtained from groundwater observation wells in the Chianan coastal plain in southern Taiwan. In this area, sedimentary aquifer systems consist of a stack of alternating sand and mud layers, over several hundred meters in thickness. Groundwater has been abstracted from these aquifers for decades, resulting in large hydraulic gradients between the shallow and deeper aquifers. Hence, vertical groundwater flow is likely enhanced across finer-grained, semi-confining units. A set of temperature–depth profiles is available from this area. Constrained by these profiles, numerical models of one-dimensional transient heat transfer were used to infer vertical fluxes of 3.3 × 10−8 to 3.9 × 10−8 m/s using thermal data from 2013 to 2016. An analytical solution was also employed that assumes steady-state conditions. Calculated fluxes using the latter approach were lower, at approximately 1.1 × 10−8 to 1.6 × 10−8 m/s. The study suggests that vertical fluxes derived from using Bredehoeft and Papadopulos’s analytical solutions result in underestimates of actual vertical seepage rates across aquitards.