Over the past two decades, methods for analyzing DNA from the environment (eDNA) have improved and can now be useful for several practical purposes, such as early detection of harmful species and ecosystem assessment. Despite this progress, eDNA is an evolving field with few established protocols, and thus still daunting to implement. Here I review two large-scale eDNA efforts and highlight how they, and eDNA in general, can be used in aquaculture. First, I will discuss the Maine-eDNA Index Sites survey that sampled eDNA monthly at 12 sites in coastal Maine over three years. Samples were metabarcoded with methods targeting bacteria, microbial eukaryotes, invertebrates, and vertebrates allowing us to explore how coastal ecosystems and aquaculture-relevant species changed seasonally, latitudinally, and across years. Then I will discuss the GOTeDNA (Guidance on optimal eDNA Sampling periods) project, which is an international effort to collate and summarize species detection data across eDNA time seriess. GOTeDNA currently provides a user-friendly Shiny app that enables practitioners to quickly identify the optimal time of year to sample many species and the eDNA methods that are best for their purposes. Overall, both Maine-eDNA and GOTeDNA provide useful insights and resources for those who seek to use emerging eDNA methods in aquaculture.