The inter-layer cooling strategy is a critical yet often-neglected process parameter in Wire Arc Additive Manufacturing (WAAM) that directly governs thermal history, solidification behaviour, and resultant build integrity. This study presents a comparative investigation of two inter-layer cooling approaches, Active Substrate Cooling (ASC) and Active Layer Cooling (ALC), during multi-layer WAAM deposition of Inconel 625 (IN625) on an SS304 substrate using a constant heat input of approximately 218 J/mm (120 A, 19.4 V, 8 mm/s). In-situ pyrometer measurements across ten deposited layers, corroborated by the Rosenthal 3D moving-point heat-source model, were used to quantify layer-wise cooling rates, thermal gradients (G), solidification velocities (R) and G/R ratios as indicators of solidification morphology. ASC exhibited a pronounced mid-wall thermal degradation, with cooling rates collapsing from 97 °C/s at layer 1 to 22 °C/s at layer 9 (1000→500 °C window), causing G/R values to fall below the columnar-to-equiaxed transition threshold (0.35-0.80 × 10⁶ K·s/m²) in layers 5–9 and introducing the risk of microstructural heterogeneity in tall builds. ALC, by contrast, sustained cooling rates of 50-109 °C/s throughout all layers, maintaining G/R ratios of 0.78-1.71 × 10⁶ K·s/m² and ensuring stable epitaxial columnar dendritic solidification across the full wall height. Primary dendrite arm spacing predictions indicate a 30–50% refinement under ALC (10-16 µm vs. 18–29 µm), directly suppressing Nb/Mo micro-segregation and Laves phase formation. Analytical residual stress estimates further suggest ALC reduces peak longitudinal stress by 20-40% relative to ASC. These findings establish ALC as a viable process-level solution to heat accumulation in nickel superalloy WAAM, enabling consistent thermal and microstructural control without sacrificing deposition continuity.