Zooplankton collection methods can differ substantially in the information produced; therefore, determining the best method or methods for a particular ecosystem is essential in understanding limnological processes. We compared results of two sampling methods, Wisconsin net vertical tows and Schindler-Patalas traps, that have been used in a long-term monitoring program in a large, shallow reservoir, Kentucky Lake, USA. Although there were differences in net mesh size and volume of water sampled, statistically similar cladoceran and copepod communities were captured by both methods. Population densities and the number of taxa collected did differ between methods, with many smaller rotifer taxa being found only in the vertical tows, but there were higher densities of larger taxa in the traps. Annual patterns were similar for most larger taxa, except that Wisconsin net tows revealed an autumn density peak for Bosmina longirostris not well-detected in the trap samples. Given the biases of each method, the Schindler-Patalas trap appears to be more efficient overall in long-term monitoring studies, particularly in shallow systems where multiple samples are taken frequently at a number of sites.