This Special Issue presents 11 research articles focused on ecology, biodiversity, and monitoring of freshwater ecosystems under increasing anthropogenic pressures. The studies cover a wide range of topics, including phytoplankton assessment using morphological and molecular approaches, ecological differentiation of oligochaete communities, and conservation of Unio crassus. Other contributions explore the application of the EPT index for water quality assessment, microplastic pollution in benthic organisms, and the genetic diversity and conservation requirements of lampreys in Croatia. Research on meiofaunal assemblages in Baiyangdian Lake (China) further advances our understanding of ecosystem health and restoration priorities. Together, these studies provide valuable insights into freshwater biodiversity and highlight the importance of integrating classical and modern approaches for effective ecological assessment and management.