A major challenge in quantifying coral reef connectivity is understanding how complex physical mechanisms influence larval dispersal across habitats and depths. Many studies show that coral spawning is not limited to surface slicks, emphasising the need to accurately model how oceanographic processes shape connectivity pathways for neutrally and negatively buoyant larvae. Scott Reef, an atoll on the Australian North West Shelf, exemplifies the importance of subsurface processes in linking spatially distinct coral communities. Tidally-driven mechanisms at Scott Reef regularly pump cool water up the outer slopes and into the reef, enhancing thermal protection for certain coral communities. Connectivity between these well-protected slope corals and the inner lagoon may be imperative for the reef’s recovery following destructive heat stress events. We used a 2D Lagrangian particle tracking model at three depths over a full spring–neap tidal cycle, examining both spawning and brooding reproductive strategies. Using Lagrangian coherent structure (LCS) analysis, we show that connectivity between the northwestern outer slopes, where subsurface cooling driven by tidal processes is most prominent, and the inner lagoon is highly dependent on both depth and tidal phase. During spring tide, weak transport barriers at depth enabled particles to penetrate much further into the lagoon than near the surface, where transport was almost entirely blocked. In contrast, neap tide transport pathways were homogeneous across depths, supporting the idea that connectivity at Scott Reef is strongly influenced by subsurface processes only active during the spring tide. These findings highlight the importance of tidal timing and vertical structure on the success of coral reproductive events. By advancing our understanding of how reef dynamics vary across depths, we can improve predictions of post-disturbance recovery and support more targeted management and rehabilitation strategies.