Actually Newton's second law is not about acceleration but about momentum. The 'real' 2nd law of Newton states that the change in momentum is equal to a force.
Remember that change in momentum = d(mv)/dt = mdv/dt + vdm/dt = sum of all forces. But for solids usually dm/dt is zero and dv/dt is of course acceleration. This results in the famous F=ma. But for fluids the term dm/dt is not necessarily zero.
So, in a case of a fluid you take a control volume stationary in space (this is actually not necessary, but makes integration a lot easier) then you apply Newton's second law by stating that the momentum flow into the volume (over it's boundaries) is equal to the momentum out of that volume plus the force applied on that volume (for example if one of the boundaries of that volume is a solid wall, but note that the pressure integrated over a boundary over which fluid flows is also a force which needs to be taken into account). If you apply this correctly than you end up with the Navier-Stokes equations.