Work requires both force and displacement. You could say that the displacement is a result of the force, which depends on the duration that the force is applied.
So work done might be small, even though a huge force has acted. If that huge force just applied at an instant, as an impulse, then the work is not as big as we would expect. But some work is still done.
How much this work, however small or big, influences a free object, is described by the work-energy theorem. This theorem combines the work $W_{total}$ done by external forces $\vec F$ on an object (the energy added to it) with the object itself (it's mass $m$) and it's mechanical state (it's speed $v$ and position $\vec s$). And that combination is done through energy conservation:
$$\begin{align}
W_{total}&=\Delta K\\
\int \vec F \cdot d\vec s&=\frac12 mv_2^2-\frac12 mv_1^2
\end{align}$$
Work is in general an integral. Meaning, it is a sum of all force-times-displacement products at every instant, however small. So at impact with the water surface in your example, the large force that acts for a very short time (it acts over a tiny displacement) is indeed included and added to the total amount of work. While the object sinks further, the fluid resistance, buoyancy force etc. add additional work.
Which that is more significant depends on many things, but in the end they must all be added together into the total work done that causes the change in kinetic energy as the theorem tells.