Khenchela, a medium-sized Algerian city situated in the semi-arid Aurès massif (Eastern Algeria, North Africa), exemplifies a growing class of rapidly urbanising cities where flood risk results less from climatic extremes per se than from the cumulative interaction of uncontrolled urban expansion, ageing drainage infrastructure, and the systematic exclusion of hydrological constraints from urban planning. This study investigates the co-production of flood vulnerability in the inter-municipal grouping of Khenchela through an integrated diachronic framework combining multi-temporal Landsat remote sensing (1985–2025), GIS-based morpho-hydrological analysis, and technical diagnosis of a 265.5 km combined sewer network. Two structurally coupled mechanisms are identified. The first is a morphological dimension characterised by a fourfold increase in built-up surface at the municipal scale (3.48 → 14.10 km²) and a more than fivefold increase at the inter-municipal scale (4.20 → 21.81 km²), progressive colonisation of natural drainage corridors, and transition from a compact radio-concentric urban form to a fragmented polycentric configuration. The second is a technical dimension embodied by a combined sewer system dimensioned for a 1998 urban perimeter, now structurally inadequate relative to current hydrological loads, as reflected by a runoff coefficient increase from C = 0.46 to C = 0.55. Field validation of 22 documented overflow points confirms 87% spatial concordance with modelled conflict zones. A CA-ANN prospective simulation (MOLUSCE/QGIS, κh = 0.87) projects a built-up surface of 28–30 km² by 2035, with a runoff coefficient exceeding 0.62 and peak discharge increases of 40–60% under RCP 4.5. The fully open-source, reproducible, and scalable methodological framework is directly applicable to comparable medium-sized cities in semi-arid North Africa and the Global South facing similar urbanisation–infrastructure mismatches.