Invertebrates are often used in biological monitoring of soil and water ecosystems. Because of the huge number of invertebrate species, sample processing (sorting and identification) is a labor-intensive and often difficult task that is prone to error. These errors can bias assessment results, which often are used by environmental managers to guide funding decisions for costly restoration measures. However, quality control of assessment results is not implemented in many freshwater monitoring programs. We conducted the first audit of an official European freshwater monitoring program based on 414 macroinvertebrate samples from streams and rivers in Germany. The samples were collected by personnel at 7 different commercial environmental laboratories using the European Union (EU) Water Framework Directive protocol. We audited 12% of all samples at 3 different levels: 1) a sorting audit, 2) an identification audit, and 3) a total audit based on both sorting and identification. The sorting audit revealed that 29% of the specimens and every 5^th taxon (20.6%) had been overlooked by the primary analyst. Differences in sorting were correlated with taxon body size (r  =  0.61, p < 0.001). The identification audit showed that >30% of taxa differed between the results of the primary analysts and auditors. Taxa considered difficult to identify were not more prone to error than were taxa considered easier to identify. Primary analysts and auditors assigned 34% of audited samples to different quality classes in ≥1 of 3 assessment modules (organic pollution, acidification, and general degradation). For 16% of the samples, these changes resulted in a different final ecological assessment. Such a high rate of differences between primary analysts and auditors could lead to ineffective allocation of several million Euros. Our results clearly illustrate the need for adequate quality control and auditing in freshwater monitoring.