Water swirls were observed in both model and prototype aquaculture tanks with bottom drains. This phenomenon was seldom replicated in studies of flow fields of water in aquaculture tanks with computational fluid dynamics. A commonality of these studies is that the linear eddy-viscosity turbulence models were employed. This study delves into the water swirls from the aspect of the generation of the turbulence kinetic energy; both the linear and nonlinear eddy-viscosity turbulence models are used, as well as a Reynolds stress turbulence model. A novel identification method is utilized to pinpoint vortex structures. Numerical results affirm the outstanding performance of the Reynolds stress model to estimate the flow fields of water in aquaculture tanks. Both the linear and nonlinear eddy-viscosity models overestimate the kinetic turbulence energy in the stagnation zone of swirls. The overestimation can be restrained by including the effect of the streamline curvature correction (SCC) to the turbulence production term. Even so, the SCC does not help to improve the estimating accuracy between the Reynolds stress tensor and the mean rate-of-strain tensor. While the nonlinear model offers some improvements, the Reynolds stress model provides a more effectvie solution. After that, we calculate the flow fields of water in aquaculture tanks with different inlet–outlet configurations with the Reynolds stress turbulence model. Both the vertical and horizontal scales of water swirls increase with inlet velocities and Froude numbers, where the Froude number is based on the bottom draining velocity and the water depth above the bottom drain. The vertical distributions of the water residence time in aquaculture tanks are shown to improve the design of tanks.