A 2DV h-adaptive finite element code for solving coupled Navier-Stokes and scalar- transport equations for application to estuarine cohesive sediment transport is described. The program is tested against a well known benchmark problem, the thermally driven cavity problem, and provides results that compare well with existing solutions, generating confidence in the coupling of the governing equations and in the h-adaptive re-meshing routines. Numerical models for varying viscosity non-Newtonian flow, flocculation and settling are described. The program is also used to solve settling in slack estuarial water. The settling speed, general form and development of the hindered settling layer is found to be close to that observed in experimental and field data, adaptivity also enables effective capture of the lutocline as it settles.