Hypertension (HTN) and hypertrophic cardiomyopathy(HCM) induce structural and functional remodelling of the left atrium (LA), contributing to atrial dysfunction and altered flow dynamics. However, the specific impact of these conditions on intra-atrial blood dynamics has not yet been well characterised. In this study, we used a semi-automated Lagrangian-tracking pipeline to quantify distinct intra-atrial flow patterns from 4D flow magnetic resonance imaging (MRI) data. This represents the first application of the approach to compare LA hemodynamics in HTN, HCM, and controls. This pipeline enables the identification and quantification of distinct intra-atrial blood flow patterns, unlike conventional qualitative assessments or global flow quantification indices. The findings demonstrate significant, common changes in LA function in both diseased groups as a result of chronic pressure overload. Both patient groups showed significantly reduced conduit flow (p < 0.001) and increased retained and residual volumes (p < 0.01), indicating impaired LA emptying and a shift toward stasis-prone flow. Particle trajectories were less curved in disease, reflecting a loss of organised vortical structures. Pulmonary venous (PV) systolic and diastolic velocities were attenuated (both p < 0.01), and PV backflow decreased (p < 0.05), consistent with reduced atrial compliance. HTN and HCM groups showed significantly altered kinetic energy (KE) curves, revealing disruption of LA energetics. Collectively, these quantitative 4D flow MRI biomarkers provide novel insight into shared patterns of atrial dysfunction in pressure-overload cardiomyopathies and may serve as non-invasive markers for disease severity.