A 3 × 3 × 3 completely randomized design was used to investigate extrusion cooking behavior and product characteristics of distillers dried grains with solubles (DDGS), protein levels, and various starch sources in a laboratory scale single screw extruder. Cassava, corn, and potato starches with varying levels of DDGS (20%, 30%, and 40% wet basis (wb)) were extruded with three different proportions of protein levels (28%, 30%, and 32% wb). The extrusion cooking was performed at a constant feed moisture content of 20% wb, barrel temperature of 120 °C, and a preset screw speed of 130 rpm (13.6 rad/s). Extrudate properties such as expansion ratio, unit density, sinking velocity, color, water absorption and solubility indices, and pellet durability index were determined to judge the suitability for various fish species. For all three starch bases, increasing the DDGS levels resulted in a significant increase in sinking velocity, redness (a*), and blueness (b*) and showed a decrease in whiteness (L*). With the increase in DDGS and protein levels, a noticeable increase was observed for unit density and pellet durability indices for cassava and potato starch extrudates. The DDGS-based extrudates produced from cassava starch with lower proportions of DDGS (20%) and protein (28%) levels exhibited better expansion and floatability. Also, the extrudates produced from corn starch with higher levels of DDGS (40%) and protein (32%) levels were more durable and possessed sinking characteristics. Overall, cassava and corn starch with lower and higher levels of DDGS could be more appropriate for the production of floating and sinking aquaculture feeds, respectively.