Historically, groundwater ecosystems were thought to harbor few species and their conservation was mainly as an exploitable water resource. In recent decades, it has become clear that many groundwater ecosystems are biodiverse, contain species absent from surface habitats, and carry out many different ecological processes that provide crucial ecosystem services beyond simply being a water source. After briefly reviewing the evolution of concepts about groundwater biodiversity, this chapter describes some approaches now being used to aid groundwater conservation, including molecular methods such as environmental DNA and metabarcoding. Data from these can be used with remotely sensed data to enhance vulnerability mapping and systematic conservation planning approaches. Future advances in groundwater conservation will include educating people about groundwater ecosystems and their often-rich troves of species that are potentially threatened by overexploitation of groundwater and by surface activities that harm the quality or quantity of recharge.