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The atmospheric moisture budget is a fundamental regulator of regional hydroclimate, yet its component-wise dynamics across India’s diverse agro-climatic zones remain poorly quantified. This study presents a comprehensive assessment of evaporation minus precipitation (E–P) variability over 1990–2024 using era reanalysis data5 reanalysis data, employing a full atmospheric moisture budget framework. The atmospheric moisture transport is decomposed into its mean (M1), and transient (M2, M4), and interaction (M3) components. This approach allows for the explicit attribution of E–P trends and anomalies to specific dynamic drivers. We also perform a decomposition of vertically integrated moisture transport into mean component, their low-frequency (LF) (>10 d) and synoptic (<10 d) scale contributions. Results reveal pronounced spatial heterogeneity: negative E–P trends dominate western India and the coast, while positive trends prevail over the Gangetic plains and Northeast, consistent with observed monsoon weakening in high-rainfall regions. Our analysis demonstrates that while mean moisture transport by mean winds establishes the climatic-scale background, transient eddy fluxes constitute a significant secondary driver, amplifying intraseasonal variability across central and northern India. Moreover, scale separation clarifies that LF oscillations modulate broad-scale convergence patterns, whereas synoptic disturbances generate sharp, localized extremes. This study offers the first mechanistic, India-wide attribution of E–P variability, linking large-scale circulation to weather-scale events. A critical finding is a widespread positive trend in transient eddy divergence (M4), indicating a strengthening moisture-export that reduces rainfall efficiency. By disentangling these drivers, our analysis provides essential insights for improving predictions of water stress and informing targeted climate adaptation strategies in this vulnerable, monsoon-dependent region.