The present invention provides a water-based coating system that can be used to form a durable, abrasion resistant, tough, protective coating on a wide range of substrates. The coating system advantageously has excellent adhesion properties and can be directly coated onto stainless steel surfaces without requiring an intervening primer layer. Primer layers or other types of coatings can be used in combination with the coating system of the present invention if desired, however. The coating system is particularly effective for protecting metal-containing substrates such as intermodal, refrigerated cargo containers. The resultant coatings are flexible and impact resistant. Being water-based, the coating compositions have lower VOC emissions and less residual odor than solvent-based compositions.