With a *really* good magnetic hand-bearing compass, up-to-date charts and a detailed survey of any local magnetic anomalies, you could triangulate off three well spread out, distinctly visible landmarks at accurately known latitude and longitude coordinates to get a position on the surface at best accurate to approx. +/-10 meters per Km of distance from the landmarks. You'd do better with DGPS in the boat which could reduce the surface position uncertainty by an order of magnitude or two. Transferring that position to the seabed in anything except shallow water is problematic due to currents and tides. In a still lake you *MIGHT* be able to maintain reasonable accuracy dropping a plumb-line.
The pros will be using something like a network of DGPS equipped sonar buoys or a towed hydrophone array with surface GPS transponders at its head and tail.