|Habitats in the anchialine ecosystem are defined as coastal ponds, pools, and caves that lack surface connections to the open ocean, but possess both seawater and freshwater influences due to subterranean connections to the ocean and groundwater. Such habitats are rare worldwide, but are concentrated in the Hawaiian Islands. Organisms that live in these habitats must cope with changing salinities, variable oxygen regimes, high levels of UV radiation, and anthropogenic effects such as pollution and invasive species. Accordingly, such organisms represent an opportunity to shed light on environmental physiology and invasive species biology. However, few studies have investigated physiology or response to invasive species in anchialine organisms. Accordingly, the objective of this dissertation is to examine the effect of natural and anthropogenic disturbances on the physiology and ecology of anchialine organisms. Chapter 1 provides an introduction to the anchialine ecosystem and outlines the specific aims of the dissertation. Chapter 2 presents a series of field and laboratory based experiments investigating how endemic Hawaiian anchialine organisms have responded to invasive fishes. Based on its results, endemic anchialine organisms largely avoid predation by invasive fishes by adopting an alternative strategy of diel migration in fish-invaded habitats. Chapter 3 provides a quantitative, statistical review of how previously-studied animals respond to changing salinity via altering gene expression. The results of this meta-analysis suggest that up-regulation of a suite of genes is typical for crustaceans undergoing salinity transfers, although studies have mostly been confined to a narrow taxonomic range of decapod brachyurans (i.e., crabs). Chapter 4 seeks to remedy this lack of knowledge by examining how the endemic Hawaiian anchialine atyid shrimp Halocaridina rubra responds to fluctuating salinity at the organismal, tissue, cellular, and molecular level. These results suggest H. rubra (and possibly other anchialine crustaceans) has continually expressed osmoregulatory mechanisms, including high, constitutive levels of osmoregulatory gene expression, which is in stark contrast to previously studied crustaceans. Chapter 5 examines how H. rubra and anchialine shrimps from the Ryukyus Archipeligo of Japan respond to low-oxygen conditions. By examining metabolic characteristics under varying oxygen regimes, it is concluded that H. rubra has gills that are specialized for osmoregulation, but not respiration, requiring a high resting ventilation rate and resulting in a strategy of oxyconformation. The other species have a different strategy more consistent with previously described mechanisms in crustaceans. Lastly, Chapter 6 provides conclusions, synthesis of the preceding chapters, and future directions.