Two methods were used to sample aquatic macroinvertebrates in three turloughs. Turloughs are systems that flood periodically from groundwater, in response to local rainfall patterns and contain rare aquatic species and assemblages. The first method used a standard pond net that was swept through the water column, while the second involved fixing a rectangular, open-bottomed box to the substrata and removing all organisms with a net. Similar overall sampling effort was applied to each method and individual box samples were found to take longer to gather than pond net samples. The box method, however, gave the maximum yield for a given sampling effort. Significantly more beetle species and individuals were recorded per unit area of bottom at all three turloughs using the box method. Multivariate analysis segregated samples, firstly according to site and secondly, with respect to method. The box method is a viable alternative to sampling with a pond net. It is more quantitative, objective, specific and reliable. This is particularly important in habitats distinguished by rare species and assemblages, and for which monitoring is driven by legislative needs.