We examined fish assemblages in isolated streambed pools in an intermittent portion of the Brazos River drainage in Texas to determine whether communities were structured in a predictable fashion by changing environmental conditions. Specific conductance, pool volume, and turbidity were significant predictors of species presence in isolated pools. The presence of the Red River pupfish Cyprinodon rubrofluviatilis increased with specific conductance and decreasedwith turbidity. The presence of the western mosquitofish Gambusia affinis, redshiner Cyprinella lutrensis, plains minnow Hybognathus placitus, smalleye shinerNotropis buccula, and sharpnose shiner N. oxyrhynchus decreased as specific conductance increased and as volume and turbidity decreased. Pools sampled throughtime showed progressive, predictable changes in environmental conditions. As pools evaporated, specific conductance increased and volume and turbidity decreased. Decreases in cyprinid presence and abundance occurred concurrently with increases in specific conductance and decreases in volume; however, cyprinodontid presence remained constant and abundance increased. These results demonstrate that changes in fish assemblage structure in drying pools are predictable. Unaltered cyprinodontid populations during pool confinement and dry-down may enable these species to expand and predominate until more benign conditions return andother species have an opportunity to recolonize pools.