The ability to adequately assess ecosystem health is essential for informed resource management. Freshwater zooplankton respond rapidly to environmental changes in pest fish populations and nutrient loads and can therefore be used to monitor ecosystem health and provide a surrogate for lake biodiversity. The Zooplankton Molecular-Based Assessment (ZooMBA) described here is a technique for assessing zooplankton communities using short fragments of DNA sequences and a recently developed, online database of reference sequences ("DNA barcodes"). Users can collect their own zooplankton samples using standard collection techniques and either pre-process samples or send samples directly to appropriate laboratory facilities for molecular analyses. Resulting data can then be used to provide accurate species inventories, or cumulatively, can be used to compute indices of lake trophic status (e.g. rotifer Trophic Level Index).