Blue mussel aquaculture’s dependence on wild-caught seed has posed considerable complications for farmers in recent years due to increasingly variable seasonal fluctuations in larval availability. Regular monitoring of the plankton community on an aquaculture lease to identify the optimal timing for seed collection can help alleviate potential seed recruitment failures and resulting financial and production losses. Recently, we developed a promising mussel larvae monitoring protocol that combines traditional plankton tow sampling with environmental RNA (eRNA) quantitative PCR (qPCR) assays that allow for the specific detection of blue mussel larvae. Here, we will discuss our monitoring results from a mussel farm in Casco Bay, ME over a nearly two-year period, compare the results of plankton tow counts vs. eRNA qPCR assay quantification, and relate these results to environmental data collected on the farm. In addition, we will describe current efforts to convert our eRNA qPCR assays into more accessible loop-mediated isothermal amplification (LAMP) assays, which do not require specialized equipment and offer a simple colorimetric result for the visual determination of presence/absence of mussel larvae in a water sample. These tools and results will not only provide stakeholders with a user-friendly and rapid method to predict the ideal timing for seed collection, but they will also result in a better understanding of the phenology of mussel larvae and the environmental variables that drive it.