In the design of offshore aquaculture net-pens, computer based models are needed in order to evaluate and optimize design criteria prior to the construction and testing of expensive prototype net-pen systems. Two fundamental criteria that must be addressed are dynamic response and reliability. Practical computer modeling methods must be capable of handling the complex fluid/pen interactions that occur in high energy open ocean environments for a broad range of net-pen designs. The resulting dynamic response and stress and stress cycling information are essential input for design modification and lifetime predictions. In the paper, the finite element method is used to predict the three-dimensional dynamic response of submerged offshore net-pens and their associated moorings. Solid-framed and pre-stressed net-pen designs are modeled using simple structural elements. The solution to the nonlinear dynamic equilibrium equations is obtained using an incremental-iterative method based on an updated Lagrangian formulation. The resulting semi-discrete equations are integrated in time using the trapezoidal rule, and full Newton-Raphson equilibrium iteration is employed during each time step. Fluid loading is implemented using the Morison equation, along with Airy wave theory. The contributions to the element stiffness matrices that arise from the fluid loading are continually updated during the iterative process. Initial validation of the finite element results for a basic cage configuration is made by comparison to experimental data obtained from a simple cage model subjected to a constant current in a flume.