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Abstract Atmospheric escape shapes exoplanet evolution and star–planet interactions, with HeI10830 Å absorption serving as a key tracer of mass loss in hot gas giants. However, transit depths vary significantly across observed systems for reasons that remain poorly understood. HD209458b, the archetypal hot-Jupiter, exhibits relatively weak HeI10830 Å and Hαabsorption, which has been interpreted as evidence for a high H/He ratio (98/2), possibly due to diffusive separation. To investigate this possibility and other processes that control these transit depths, we reassess excitation and de-excitation rates for metastable helium and explore the impact of diffusion processes, stellar activity, and tidal forces on the upper atmosphere and transit depths using a model framework spanning the whole atmosphere. Our model reproduces the observed HeItransit depth and Hαupper limit, showing strong diffusive separation. We match the observations assuming a photoelectron efficiency of 20%–40%, depending on the composition of the atmosphere, corresponding to mass-loss rates of 1.9–3 × 10¹⁰g s⁻¹. We find that the HeI10830 Å transit depth is sensitive to both stellar activity and diffusion processes, while Hαis largely unaffected due to its strong dependence on Lyαexcitation. These differences may help explain the system-to-system scatter seen in population-level studies of the HeIline. While HeIdata alone may not tightly constrain mass-loss rates or temperatures, they do confirm atmospheric escape and help narrow the viable parameter space when interpreted with physically motivated models. Simultaneous observations of HeI, Hα, and stellar activity indicators provide powerful constraints on upper atmosphere dynamics and composition, even in the absence of full transmission spectra.