This Special Issue contains 31 papers that collectively advance understanding of nonlinear dynamics, resilience, and regime shifts in aquatic communities and ecosystems. These papers make two basic contributions: 1) They further advance the study of resilience and regime shifts from theoretical to empirical science. 2) They expand the systems and characteristics that we can understand through the lenses of nonlinear dynamics, resilience, and regime shifts, demonstrating that these concepts are broadly applicable throughout the aquatic environment. Within this context, several themes emerge, including processes of disturbance and recovery, changing trends, contingent and historical attributes, extreme events, compensation, and synchronization. These topics are not the result of any design by us as editors but rather reflect the diverse topical interests of the field resulting from the open submission of papers to the Special Issue. Collectively, these themes represent many of the important ideas driving modern study of aquatic systems, especially in response to large-scale environmental change.