My long-term goal is improving our understanding of interactions between sub-grid scale models and numerical errors, which affect simulation skill for physical and biological processes in estuaries and coastal ocean environments. For prognostic simulations, slow accumulation of truncation-level errors will progressively distort model results. Present sub-grid scale models selectively address certain processes (e.g. turbulence) while neglecting other processes (e.g. small-scale internal waves, particulate nature of algae). As small-scale nonlinear errors can accumulate over time, understanding the errors and modeling the neglected processes are critical issues in improving our prognostic skill.