Sampling in springs has several technical problems due to their reduced dimensions and habitat heterogeneity. A standardized quantitative method for sampling crenic macroinvertebrates has never been proposed. The aim of this study was to compare different sampling methods and consider their environmental impacts. First, we present a review of sampling methods found in the literature and discuss their advantages and disadvantages with respect to selective collection of the target community and habitat disturbance. Altogether, 10 different methods have been reported, the use of nets being the most common protocol. Second, we report the results of macroinvertebrate samplings performed in three springs, each surveyed twice, using three different methods (multi-habitat proportional hand net, baited traps, and vegetation washing), in order to compare their effectiveness in collecting macroinvertebrates. Overall, 32 macroinvertebrate taxa, mostly identified at family level, were collected in the sampled springs. Significant differences in abundances were found using different methods, while results for community structure were comparable between the hand net sampling and the combined use of the other two methods, notwithstanding slight differences in the composition of Coleoptera and Diptera assemblages. The hand net, with a multi-habitat proportional approach, yielded more thorough results, making it suitable for biodiversity inventories but having some potentially negative effects on spring habitats. Traps and vegetation washing are also reliable methods with negligible impacts on spring ecosystems that can be conveniently used in ecological studies.