Adjacent intensive agriculture disturbs the natural condition of wetlands. However, to assess the effect of this agriculture on wetlands, few studies have used indices based on aquatic invertebrates. Multi-metric indices (MMIs) have been successfully used to assess freshwater ecosystems worldwide and are an important management tool, but little is known about their applicability in the Sanjiang Plain, Northeast China. In this study, we developed a MMIs for aquatic invertebrates to assess freshwater wetlands in this region. The aquatic invertebrate assemblages were sampled in 27 wetlands in the Sanjiang Plain that included those in natural reserves and those affected by adjacent, intensive agriculture. Twenty-four candidate metrics were initially reviewed and screened before four core metrics were selected: total number of taxa, number of Hemiptera taxa, proportion of Gastropoda, and proportion of predators. Mann-Whitney U tests, Box and Whisker plots, correlation analyses, and redundant metric tests were used to assess the ability of metrics to distinguish among reference and impaired wetlands. Four ordinal rating categories for wetland were defined: poor, fair, good, and excellent. Of the impaired freshwater wetlands, 76.2% were in poor or fair categories. The MMIs was robust in discriminating reference wetlands from impaired wetlands and therefore have potential as a biomonitoring tool to assess the condition and to guide the restoration efforts of freshwater wetlands in Northeast China.